I ran into some issues with MiKTeX 2.9 so I uninstalled and reinstalled it (using net installer), in the hopes that the issues would be resolved. Instead MiKTeX seems to be completely broken now; when I try to compile a document (which has compiled successfully just this morning), TeXworks is giving me this error message:

This is pdfTeX, Version 3.14159265-2.6-1.40.19 (MiKTeX 2.9.6840 64-bit)

Sorry, but pdflatex did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\user\AppData\Local\MiKTeX\2.9\miktex\log\pdflatex.log

Sorry, but "MiKTeX Compiler Driver" did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\user\AppData\Local\MiKTeX\2.9\miktex\log\texify.log

I will paste the contents of the logs into the end of this post. I have tried uninstalling again, deleting all folders related to MiKTeX in Program Files and AppData, restarting my laptop and reinstalling it again, but nothing seems to be working. Compiling it in the command line doesn't work either. I am relatively new to using LaTeX and out of ideas, I would be very thankful if someone can help me with this issue.

This is the content of pdflatex.log:

2018-10-05 02:19:48,194+0200 INFO  pdflatex - starting with command line: pdflatex --synctex=1 C:/Users/user/Documents/university/presentation\slide1.tex
2018-10-05 02:19:48,206+0200 INFO  pdflatex - allowing known shell commands
2018-10-05 02:19:48,208+0200 INFO  pdflatex - enabling input (output) from (to) processes
2018-10-05 02:19:48,292+0200 INFO  pdflatex - going to create file: pdflatex.fmt
2018-10-05 02:19:49,704+0200 ERROR pdflatex - C:\Programme\MiKTeX_2.9\miktex\bin\x64\initexmf.exe did not succeed; exitCode: 1
2018-10-05 02:19:49,704+0200 ERROR pdflatex - output:
2018-10-05 02:19:49,704+0200 ERROR pdflatex - 

Sorry, but "MiKTeX Configuration Utility" did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\user\AppData\Local\MiKTeX\2.9\miktex\log\initexmf.log

2018-10-05 02:19:49,706+0200 FATAL pdflatex - The memory dump file could not be found.
2018-10-05 02:19:49,707+0200 FATAL pdflatex - Info: fileName="pdflatex.fmt"
2018-10-05 02:19:49,707+0200 FATAL pdflatex - Source: Libraries\MiKTeX\TeXAndFriends\texmfapp.cpp
2018-10-05 02:19:49,707+0200 FATAL pdflatex - Line: 690
2018-10-05 02:19:49,708+0200 INFO  pdflatex - finishing with exit code 1

The content of texify.log:

2018-10-05 02:19:12,237+0200 INFO  texify - starting with command line: C:\Programme\MiKTeX_2.9\miktex\bin\x64\texify.exe --pdf --synctex=1 --clean slide1.tex
2018-10-05 02:19:12,255+0200 INFO  texify - running 'initexmf' to refresh the file name database
2018-10-05 02:19:18,520+0200 INFO  texify - running 'initexmf' to create font map files
2018-10-05 02:19:47,751+0200 INFO  texify - starting with command line: C:\Programme\MiKTeX_2.9\miktex\bin\x64\texify.exe --pdf --synctex=1 --clean slide1.tex
2018-10-05 02:19:49,735+0200 FATAL texify - TeX engine failed for some reason.
2018-10-05 02:19:49,735+0200 FATAL texify - Info: 
2018-10-05 02:19:49,735+0200 FATAL texify - Source: Programs\MiKTeX\texify\mcd.cpp
2018-10-05 02:19:49,735+0200 FATAL texify - Line: 1476

pdflatex.log refers to initexmf.log, which is:

2018-10-05 02:19:12,553+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:19:12,553+0200 INFO  initexmf - Operating on the private (per-user) MiKTeX setup
2018-10-05 02:19:12,554+0200 INFO  initexmf - starting with command line: initexmf --enable-installer --quiet --update-fndb
2018-10-05 02:19:12,576+0200 INFO  initexmf - Creating fndb for user root directory (C:\Users\user\AppData\Roaming\MiKTeX\2.9)...
2018-10-05 02:19:12,625+0200 INFO  initexmf - Creating fndb for user root directory (C:\Users\user\AppData\Local\MiKTeX\2.9)...
2018-10-05 02:19:12,678+0200 INFO  initexmf - Skipping common root directory (C:\ProgramData\MiKTeX\2.9)...
2018-10-05 02:19:12,679+0200 INFO  initexmf - Skipping common root directory (C:\Programme\MiKTeX_2.9)...
2018-10-05 02:19:18,500+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:19:18,778+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:19:18,778+0200 INFO  initexmf - Operating on the private (per-user) MiKTeX setup
2018-10-05 02:19:18,778+0200 INFO  initexmf - starting with command line: initexmf --enable-installer --quiet --mkmaps
2018-10-05 02:19:18,798+0200 INFO  initexmf - running: mkfntmap --enable-installer
2018-10-05 02:19:48,687+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:19:48,687+0200 INFO  initexmf - Operating on the private (per-user) MiKTeX setup
2018-10-05 02:19:48,687+0200 INFO  initexmf - starting with command line: initexmf --enable-installer --dump-by-name=pdflatex --engine=pdftex
2018-10-05 02:19:48,693+0200 INFO  initexmf - running: miktex-makefmt.exe --engine=pdftex --dest-name=pdflatex --no-dump pdflatex.ini --engine-option=-tcx=cp227.tcx --enable-installer
2018-10-05 02:19:49,678+0200 ERROR initexmf - sub-process error output has been saved to 'C:\Users\user\AppData\Local\MiKTeX\2.9\miktex\log\miktex-makefmt_2018-10-05-021949.out'
2018-10-05 02:19:49,679+0200 FATAL initexmf - The executed process did not succeed.
2018-10-05 02:19:49,679+0200 FATAL initexmf - Info: fileName="C:\Programme\MiKTeX_2.9\miktex\bin\x64\miktex-makefmt.exe", exitCode="1"
2018-10-05 02:19:49,679+0200 FATAL initexmf - Source: 
2018-10-05 02:19:49,679+0200 FATAL initexmf - Line: 0

EDIT: This is miktex-makefmt_2018-10-05-021949.out

Running miktex-pdftex.exe...
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (MiKTeX 2.9.6840 64-bit) (INITEX)

Sorry, but miktex-pdftex.exe did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\user\AppData\Local\MiKTeX\2.9\miktex\log\miktex-pdftex.log


Sorry, but miktex-makefmt did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\user\AppData\Local\MiKTeX\2.9\miktex\log\miktex-makefmt.log

This is miktex-pdftex.log:

2018-10-05 02:33:07,207+0200 INFO  miktex-pdftex - finishing with exit code 1
2018-10-05 02:34:14,811+0200 INFO  miktex-pdftex - starting with command line: miktex-pdftex.exe --miktex-enable-installer --initialize --interaction=nonstopmode --halt-on-error --alias=pdflatex --job-name=pdflatex -tcx=cp227.tcx --enable-etex pdflatex.ini
2018-10-05 02:34:14,821+0200 INFO  miktex-pdftex - allowing known shell commands
2018-10-05 02:34:14,822+0200 INFO  miktex-pdftex - enabling input (output) from (to) processes
2018-10-05 02:34:14,871+0200 FATAL miktex-pdftex - Windows API error 5: Zugriff verweigert

2018-10-05 02:34:14,871+0200 FATAL miktex-pdftex - Info: path="C:\Programme\MiKTeX_2.9\tex\latex\00miktex\pdflatex.ini"
2018-10-05 02:34:14,871+0200 FATAL miktex-pdftex - Source: Libraries\MiKTeX\Core\PathName\PathName.cpp
2018-10-05 02:34:14,871+0200 FATAL miktex-pdftex - Line: 156
2018-10-05 02:34:14,871+0200 INFO  miktex-pdftex - finishing with exit code 1
2018-10-05 02:36:59,571+0200 INFO  miktex-pdftex - starting with command line: miktex-pdftex.exe --miktex-enable-installer --initialize --interaction=nonstopmode --halt-on-error --alias=pdflatex --job-name=pdflatex -tcx=cp227.tcx --enable-etex pdflatex.ini
2018-10-05 02:36:59,596+0200 INFO  miktex-pdftex - allowing known shell commands
2018-10-05 02:36:59,597+0200 INFO  miktex-pdftex - enabling input (output) from (to) processes
2018-10-05 02:36:59,665+0200 FATAL miktex-pdftex - Windows API error 5: Zugriff verweigert

2018-10-05 02:36:59,665+0200 FATAL miktex-pdftex - Info: path="C:\Programme\MiKTeX_2.9\tex\latex\00miktex\pdflatex.ini"
2018-10-05 02:36:59,665+0200 FATAL miktex-pdftex - Source: Libraries\MiKTeX\Core\PathName\PathName.cpp
2018-10-05 02:36:59,665+0200 FATAL miktex-pdftex - Line: 156
2018-10-05 02:36:59,666+0200 INFO  miktex-pdftex - finishing with exit code 1

This is miktex-makefmt.log:

2018-10-05 02:19:49,033+0200 INFO  miktex-makefmt - starting with command line: miktex-makefmt.exe --engine=pdftex --dest-name=pdflatex --no-dump pdflatex.ini --engine-option=-tcx=cp227.tcx --enable-installer
2018-10-05 02:19:49,047+0200 INFO  makefmt - found input file: C:\Programme\MiKTeX_2.9\tex\latex\00miktex\pdflatex.ini
2018-10-05 02:19:49,047+0200 INFO  makefmt - Creating the pdflatex format file...
2018-10-05 02:19:49,078+0200 INFO  makefmt - Running miktex-pdftex.exe...
2018-10-05 02:19:49,079+0200 INFO  makefmt - running: miktex-pdftex.exe --miktex-enable-installer --initialize --interaction=nonstopmode --halt-on-error --alias=pdflatex --job-name=pdflatex -tcx=cp227.tcx --enable-etex pdflatex.ini
2018-10-05 02:19:49,657+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:19:49,657+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:19:49,657+0200 FATAL miktex-makefmt - Info: 
2018-10-05 02:19:49,657+0200 FATAL miktex-makefmt - Source: 
2018-10-05 02:19:49,657+0200 FATAL miktex-makefmt - Line: 0
2018-10-05 02:33:06,845+0200 INFO  miktex-makefmt - starting with command line: miktex-makefmt.exe --engine=pdftex --dest-name=pdflatex --no-dump pdflatex.ini --engine-option=-tcx=cp227.tcx --enable-installer
2018-10-05 02:33:06,846+0200 WARN  miktex-makefmt - running with administrator privileges
2018-10-05 02:33:06,858+0200 INFO  makefmt - found input file: C:\Programme\MiKTeX_2.9\tex\latex\00miktex\pdflatex.ini
2018-10-05 02:33:06,860+0200 INFO  makefmt - Creating the pdflatex format file...
2018-10-05 02:33:06,870+0200 INFO  makefmt - Running miktex-pdftex.exe...
2018-10-05 02:33:06,871+0200 INFO  makefmt - running: miktex-pdftex.exe --miktex-enable-installer --initialize --interaction=nonstopmode --halt-on-error --alias=pdflatex --job-name=pdflatex -tcx=cp227.tcx --enable-etex pdflatex.ini
2018-10-05 02:33:07,249+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:33:07,249+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:33:07,249+0200 FATAL miktex-makefmt - Info: 
2018-10-05 02:33:07,249+0200 FATAL miktex-makefmt - Source: 
2018-10-05 02:33:07,249+0200 FATAL miktex-makefmt - Line: 0
2018-10-05 02:34:14,497+0200 INFO  miktex-makefmt - starting with command line: miktex-makefmt.exe --engine=pdftex --dest-name=pdflatex --no-dump pdflatex.ini --engine-option=-tcx=cp227.tcx --enable-installer
2018-10-05 02:34:14,497+0200 INFO  makefmt - found input file: C:\Programme\MiKTeX_2.9\tex\latex\00miktex\pdflatex.ini
2018-10-05 02:34:14,514+0200 INFO  makefmt - Creating the pdflatex format file...
2018-10-05 02:34:14,525+0200 INFO  makefmt - Running miktex-pdftex.exe...
2018-10-05 02:34:14,525+0200 INFO  makefmt - running: miktex-pdftex.exe --miktex-enable-installer --initialize --interaction=nonstopmode --halt-on-error --alias=pdflatex --job-name=pdflatex -tcx=cp227.tcx --enable-etex pdflatex.ini
2018-10-05 02:34:14,920+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:34:14,920+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:34:14,920+0200 FATAL miktex-makefmt - Info: 
2018-10-05 02:34:14,920+0200 FATAL miktex-makefmt - Source: 
2018-10-05 02:34:14,920+0200 FATAL miktex-makefmt - Line: 0
2018-10-05 02:36:59,236+0200 INFO  miktex-makefmt - starting with command line: miktex-makefmt.exe --engine=pdftex --dest-name=pdflatex --no-dump pdflatex.ini --engine-option=-tcx=cp227.tcx --enable-installer
2018-10-05 02:36:59,259+0200 INFO  makefmt - found input file: C:\Programme\MiKTeX_2.9\tex\latex\00miktex\pdflatex.ini
2018-10-05 02:36:59,260+0200 INFO  makefmt - Creating the pdflatex format file...
2018-10-05 02:36:59,280+0200 INFO  makefmt - Running miktex-pdftex.exe...
2018-10-05 02:36:59,280+0200 INFO  makefmt - running: miktex-pdftex.exe --miktex-enable-installer --initialize --interaction=nonstopmode --halt-on-error --alias=pdflatex --job-name=pdflatex -tcx=cp227.tcx --enable-etex pdflatex.ini
2018-10-05 02:36:59,714+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:36:59,714+0200 FATAL miktex-makefmt - miktex-pdftex.exe failed on pdflatex.ini.
2018-10-05 02:36:59,714+0200 FATAL miktex-makefmt - Info: 
2018-10-05 02:36:59,714+0200 FATAL miktex-makefmt - Source: 
2018-10-05 02:36:59,714+0200 FATAL miktex-makefmt - Line: 0

EDIT:

Well I hope you learned that "simply reinstall everything" is not the best strategy to solve problems. miktex can't create the format file, so you need to find out why. Go to the miktex console, settings -> tab format. Select pdflatex and click on build. If it fails you perhaps get the real log-file. - Ulrike Fischer

After doing this, the build failed, the error message refers to this log initexmf_admin.log:

2018-10-05 02:14:23,267+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:14:23,267+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:14:23,267+0200 INFO  initexmf - starting with command line: initexmf --rmfndb --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:14:23,267+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:14:23,670+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:14:23,670+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:14:23,670+0200 INFO  initexmf - starting with command line: initexmf --update-fndb --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:14:23,670+0200 INFO  initexmf - Skipping user root directory (C:\Users\user\AppData\Roaming\MiKTeX\2.9)...
2018-10-05 02:14:23,670+0200 INFO  initexmf - Skipping user root directory (C:\Users\user\AppData\Local\MiKTeX\2.9)...
2018-10-05 02:14:23,670+0200 INFO  initexmf - Creating fndb for common root directory (C:\ProgramData\MiKTeX\2.9)...
2018-10-05 02:14:23,717+0200 INFO  initexmf - Creating fndb for common root directory (C:\Programme\MiKTeX_2.9)...
2018-10-05 02:14:38,025+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:14:38,344+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:14:38,344+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:14:38,344+0200 INFO  initexmf - starting with command line: initexmf --force --mklinks --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:14:38,750+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:14:39,078+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:14:39,078+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:14:39,078+0200 INFO  initexmf - starting with command line: initexmf --mkmaps --mklangs --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:14:39,078+0200 INFO  initexmf - Creating language.dat, language.dat.lua and language.def...
2018-10-05 02:14:39,141+0200 INFO  initexmf - running: mkfntmap --verbose --admin --disable-installer
2018-10-05 02:18:07,080+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:18:07,395+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:18:07,395+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:18:07,395+0200 INFO  initexmf - starting with command line: initexmf --default-paper-size=A4 --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:18:07,442+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:18:07,754+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:18:07,754+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:18:07,754+0200 INFO  initexmf - starting with command line: initexmf --set-config-value=[MPM]AutoInstall=1 --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:18:07,785+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:18:08,113+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:18:08,113+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:18:08,113+0200 INFO  initexmf - starting with command line: initexmf --update-fndb --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:18:08,113+0200 INFO  initexmf - Skipping user root directory (C:\Users\user\AppData\Roaming\MiKTeX\2.9)...
2018-10-05 02:18:08,113+0200 INFO  initexmf - Skipping user root directory (C:\Users\user\AppData\Local\MiKTeX\2.9)...
2018-10-05 02:18:08,145+0200 INFO  initexmf - Creating fndb for common root directory (C:\ProgramData\MiKTeX\2.9)...
2018-10-05 02:18:08,207+0200 INFO  initexmf - Creating fndb for common root directory (C:\Programme\MiKTeX_2.9)...
2018-10-05 02:18:22,365+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:18:22,677+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:18:22,677+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:18:22,677+0200 INFO  initexmf - starting with command line: initexmf --register-shell-file-types --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:18:22,724+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:18:23,096+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:18:23,096+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:18:23,096+0200 INFO  initexmf - starting with command line: initexmf --modify-path --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:18:23,269+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 02:18:23,597+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 02:18:23,597+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 02:18:23,597+0200 INFO  initexmf - starting with command line: initexmf --report --admin --log-file=C:\Programme\MiKTeX_2.9\miktex/config\uninst.log --disable-installer --verbose
2018-10-05 02:18:31,263+0200 INFO  initexmf - finishing with exit code 0
2018-10-05 09:03:58,226+0200 INFO  initexmf - starting: MiKTeX Configuration Utility 2.9.6811 (MiKTeX 2.9.6840 64-bit)
2018-10-05 09:03:58,226+0200 INFO  initexmf - Operating on the shared (system-wide) MiKTeX setup
2018-10-05 09:03:58,226+0200 INFO  initexmf - starting with command line: initexmf --admin --dump=pdflatex
2018-10-05 09:03:58,241+0200 INFO  initexmf - running: miktex-makefmt.exe --engine=pdftex --dest-name=pdflatex --no-dump pdflatex.ini --engine-option=-tcx=cp227.tcx --admin --enable-installer
2018-10-05 09:03:59,101+0200 ERROR initexmf - sub-process error output has been saved to 'C:\ProgramData\MiKTeX\2.9\miktex\log\miktex-makefmt_2018-10-05-090359.out'
2018-10-05 09:03:59,101+0200 FATAL initexmf - The executed process did not succeed.
2018-10-05 09:03:59,101+0200 FATAL initexmf - Info: fileName="C:\Programme\MiKTeX_2.9\miktex\bin\x64\miktex-makefmt.exe", exitCode="1"
2018-10-05 09:03:59,101+0200 FATAL initexmf - Source: 
2018-10-05 09:03:59,101+0200 FATAL initexmf - Line: 0

EDIT:

Damn, looks like miktex no longer saves the pdftex log somewhere. Open a command line in some empty test folder and then run pdftex --ini --enable-etex pdflatex.ini this should hopefully write a pdflatex.log in this folder. Or you can at least see in the terminal where it stops. – Ulrike Fischer

The resulting pdflatex.log:

2018-10-05 09:45:12,618+0200 INFO  pdftex - starting with command line: pdftex --ini --enable-etex pdflatex.ini
2018-10-05 09:45:12,618+0200 INFO  pdftex - allowing known shell commands
2018-10-05 09:45:12,618+0200 INFO  pdftex - enabling input (output) from (to) processes
2018-10-05 09:45:12,649+0200 FATAL pdftex - Windows API error 5: Zugriff verweigert

2018-10-05 09:45:12,649+0200 FATAL pdftex - Info: path="C:\Programme\MiKTeX_2.9\tex\latex\00miktex\pdflatex.ini"
2018-10-05 09:45:12,649+0200 FATAL pdftex - Source: Libraries\MiKTeX\Core\PathName\PathName.cpp
2018-10-05 09:45:12,649+0200 FATAL pdftex - Line: 156
2018-10-05 09:45:12,665+0200 INFO  pdftex - finishing with exit code 1
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    Well I hope you learned that "simply reinstall everything" is not the best strategy to solve problems. miktex can't create the format file, so you need to find out why. Go to the miktex console, settings -> tab format. Select pdflatex and click on build. If it fails you perhaps get the real log-file. – Ulrike Fischer Oct 5 at 6:58
  • Thank you for your answer; the build failed and created a new log, which is too long to add here, I will have to add it to the main post as another edit it seems? – u_niuniu Oct 5 at 7:08
  • Damn, looks like miktex no longer saves the pdftex log somewhere. Open a command line in some empty test folder and then run pdftex --ini --enable-etex pdflatex.ini this should hopefully write a pdflatex.log in this folder. Or you can at least see in the terminal where it stops. – Ulrike Fischer Oct 5 at 7:35
  • @Ulrike Fischer It did not write pdflatex.log into the same folder, but yes there was a new log in the log-folder (which is too long for a comment reply yet again). The terminal output was simply this: Sorry, but pdftex did not succeed. The log file hopefully contains the information to get MiKTeX going again: C:\Users\user\AppData\Local\MiKTeX\2.9\miktex\log\pdftex.log – u_niuniu Oct 5 at 7:49
  • Sorry but in which temporary folder did you try to run the command? But it looks as if pdftex is no allowed to run at all. Do you have some aggressive firewall or virus protection software? – Ulrike Fischer Oct 5 at 7:53

This issue has been resolved by Ulrike Fischer's last suggestion:

Sorry I can't help you. It is some access problem on your pc. You could try to reinstall in your user account in single user mode in some folder C:\miktex. Or try texlive instead. – Ulrike Fischer

I uninstalled and reinstalled it again. I ran the installer as administrator (like several times before) but changed from the default setting "for all users" to "this user only" and put it into C:\MiKTeX2.9 just to be safe. Now it is back and running again! Thank you so much!

  • Tex systems have traditionally suffered for non American nix issues, whilst most Linux users avoid paths with spaces or non Latin characters, many windows users now expect LFN's will work with Unicode in their locale. By reducing the path to simply upper lower and numerals you avoid any packages tripping over. even the decimal between 2 and 9 can potentially cause issues with path parsing/translation/substitution. However if its working well don't fix it. By running as single user install rather than administrator and user you halve your problems. – KJO Oct 5 at 13:52

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