I had the same problem. I tried various things and the following helped although I didn't know if any steps were unneeded.
Did these steps from https://wiki.lyx.org/Layouts/Layouts#toc1
If all or most layouts are missing from LyX in Windows 8 (and possibly Windows 7) files need to be copied from the application directory to the users directory. This was used with LyX 2.1.1.
- Copy the files in C:/Program Files (x86)//Resources/layouts/
- Paste the files into C:/Users//AppData/Roaming//layouts/
- You will have to view hidden files in order to see the AppData folder.
- In command prompt, run texhash or C:/Program Files (x86)//miktex/bin/texhash.exe
- Then, in LyX click Tools > Reconfigure; when finished restart LyX. The layouts should become available.
Started MiKTex Package Manager (Admin) At one point it complained about an invalid repository so change repository source
Started the MiKTeX Package Manager and installed some packages of the thousands available.
In DOS window, ran “texhash”
In Lyx, do Tools -> Reconfigure
Repeat steps 3., 4., and 5. as needed.
Hope that helps.
For MacOS users:
- Install the full version of MacTeX.
sudo texhashin terminal.
- Run LyX->Tools->Reconfigure
This will enable most cls articles already contained in MacTeX but not all.