How do you resolve the aux file confusing citations?

Question

I am writing a second version of a book and was provided a .tex file of first edition citations as \bibitem entries from the publisher (shortened version below).

    \makeatletter%
    \renewenvironment{thebibliography}[1]
         {\section*{\bibname
            \@mkboth{\MakeUppercase\bibname}{\MakeUppercase\bibname}}%
          \list{\@biblabel{\@arabic\c@enumiv}}%
               {\settowidth\labelwidth{\@biblabel{#1}}%
                \leftmargin\labelwidth
                \advance\leftmargin\labelsep
                \@openbib@code
                \usecounter{enumiv}%
                \let\p@enumiv\@empty
                \renewcommand\theenumiv{\@arabic\c@enumiv}}%
          \sloppy
          \clubpenalty4000
          \@clubpenalty \clubpenalty
          \widowpenalty4000%
          \sfcode`\.\@m}
         {\def\@noitemerr
           {\@latex@warning{Empty `thebibliography' environment}}%
          \endlist}
    \makeatother%
    
    
    \chapter{}\label{app:A}
    
    \def\bibname{REFERENCES}
    
    \begin{thebibliography}{100}
    \bibitem{bib1}Erdman, A. G., and Sandor, G. N., 1997, \textit{Mechanism Design: Analysis and Synthesis,} Vol. 1, 3rd Ed., Prentice Hall, Upper Saddle River, NJ.
    
    \bibitem{bib2}Shigley, J.E., and Uicker, J. J., 1995, \textit{Theory of Machines and Mechanisms,} 2nd Ed., McGraw-Hill, New York.
    
    \bibitem{bib3}Howell, L. L., and Midha, A., 1994, ``A Method for the Design of Compliant Mechanisms with Small-Length Flexural Pivots,'' \textit{Journal of Mechanical Design,} Trans. ASME, Vol. 116, No. 1, pp. 280--290.

\end{thebibliography}

After running the citations through the text2bib script at https://text2bib.economics.utoronto.ca/, I had myself a .bib file with each publication named "bib1," "bib2", etc., the names of which correlate to the citations in the .tex files also provided by the publisher.

The main file (abbreviated below) references the new .bib file and comments out the \bibitem list provided by the publisher.

\documentclass[a4paper,fleqn]{book}%

\usepackage{cite}  
\bibliographystyle{asmems4}

\begin{document}%

\include{c01}
\include{c02}
\include{c03}
\include{c04}
\include{c05}
\include{c06}
\include{c07}
\include{c08}
\include{c09}
\include{c10}
\include{c11}
\appendix
\bibliography{zzbib}
%\include{b01}

\end{document}

When compiling, the citations all seem to appear, but I get a massive error that continues (only the first portion is shown here):

: \citation{BIB38 : } I'm skipping whatever remains of this command Case mismatch error between cite keys BIB58 and bib58 ---line 72 of file c01.aux : \citation{BIB58 : } I'm skipping whatever remains of this command Case mismatch error between cite keys BIB70 and bib70 ---line 73 of file c01.aux : \citation{BIB70 : } I'm skipping whatever remains of this command A level-1 auxiliary file: c02.aux A level-1 auxiliary file: c03.aux A level-1 auxiliary file: c04.aux A level-1 auxiliary file: c05.aux Case mismatch error between cite keys BIB3 and bib3 ---line 18 of file c05.aux

I am pretty familiar with general LaTeX issues but know basically nothing about what the aux file is doing here. Any suggestions on how to clear this would be beneficial. Just hoping I don't need to rename all the citations.

Thanks!

Update: Forgive me if I am not following format well. This is my first post.

I'm adding the .bib file (just a couple examples for brevity, the rest is duplicated throughout, unless you'd like me to share it all).

@book{bib1,
address = {Upper Saddle River, NJ},
author = {Erdman, A. G. and Sandor, G. N.},
edition = {3rd},
publisher = {Prentice Hall},
title = {Mechanism Design: Analysis and Synthesis},
volume = {1},
year = {1997},
}

@book{bib2,
address = {New York},
author = {Shigley, J. E. and Uicker, J. J.},
edition = {2nd},
publisher = {McGraw-Hill},
title = {Theory of Machines and Mechanisms},
year = {1995},
}

@article{bib3,
author = {Howell, L. L. and Midha, A.},
journal = {Journal of Mechanical Design},
number = {1},
pages = {280-290},
title = {A Method for the Design of Compliant Mechanisms with Small-Length Flexural Pivots},
volume = {116},
year = {1994},
unidentified = {Trans. ASME},
}

Another update: After clearing the cache, upon a first recompile the number of errors jumps and none of the citations, figures, or any labels are recognized. (Example in figure).

If I recompile again, the figures and section labels are somehow now found but the bib## names are still said to not be found in the bibliography. Note that this is referring to the lowercase bib##.

After a third recompile, the errors drop again, but now the errors say that the BIB## (note capital BIB) are not in the bibliography.

Update: Here is a sample aux file for Chapter 1 (C01.tex). Note how it goes from lowercase bib to uppercase BIB. I suspect this is related to the issue.

\relax 
\citation{bib1,bib2}
\citation{bib3}
\citation{bib3}
\citation{bib4,bib5}
\@writefile{toc}{\contentsline {chapter}{\numberline {1}INTRODUCTION}{1}{}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{chap:1}{{1}{1}}
\@writefile{toc}{\contentsline {section}{\numberline {1.1}ADVANTAGES OF COMPLIANT MECHANISMS}{1}{}\protected@file@percent }
\newlabel{sec:1.1}{{1.1}{1}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.1}{\ignorespaces Examples of rigid-link mechanisms: (a) part of a reciprocating engine, and (b) Vise Grip.}}{1}{}\protected@file@percent }
\newlabel{fig:1.1}{{1.1}{1}}
\citation{bib6,bib7}
\citation{bib8,bib9}
\citation{bib6}
\citation{bib7}
\citation{bib6}
\citation{bib7}
\citation{bib4}
\citation{bib4}
\@writefile{lof}{\contentsline {figure}{\numberline {1.2}{\ignorespaces Examples of compliant mechanisms: (a) crimping mechanism (from \cite  {bib3}), and (b) parallel-guiding mechanism.}}{2}{}\protected@file@percent }
\newlabel{fig:1.2}{{1.2}{2}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.3}{\ignorespaces (a) Compliant overrunning clutch, and (b) its rigid-body counterpart shown disassembled. (From \cite  {bib6} and \cite  {bib7}.)}}{2}{}\protected@file@percent }
\newlabel{fig:1.3}{{1.3}{2}}
\citation{bib10,bib11,bib12,bib13,bib14,bib15,bib16,bib17,bib18,bib19}
\@writefile{lof}{\contentsline {figure}{\numberline {1.4}{\ignorespaces (a) Compliant crimping mechanism developed by AMP Inc., and (b) its rigid-body counterpart. Because of symmetry, only half the mechanism is shown. (From \cite  {bib4}.)}}{3}{}\protected@file@percent }
\newlabel{fig:1.4}{{1.4}{3}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.5}{\ignorespaces Example of a high-precision compliant mechanism.}}{3}{}\protected@file@percent }
\newlabel{fig:1.5}{{1.5}{3}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.6}{\ignorespaces Compliant die grippers used to hold a die during process in several different harsh chemicals.}}{3}{}\protected@file@percent }
\newlabel{fig:1.6}{{1.6}{3}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.7}{\ignorespaces Compliant constant-force robot end effector.}}{4}{}\protected@file@percent }
\newlabel{fig:1.7}{{1.7}{4}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.8}{\ignorespaces Compliant pliers, or Compliers, fishhook removal pliers.}}{4}{}\protected@file@percent }
\newlabel{fig:1.8}{{1.8}{4}}
\@writefile{toc}{\contentsline {section}{\numberline {1.2}CHALLENGES OF COMPLIANT MECHANISMS}{4}{}\protected@file@percent }
\newlabel{sec:1.2}{{1.2}{4}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.9}{\ignorespaces Compliant parallel motion bicycle brakes.}}{4}{}\protected@file@percent }
\newlabel{fig:1.9}{{1.9}{4}}
\citation{bib20}
\citation{bib21}
\citation{bib23}
\citation{bib24,bib25}
\citation{bib22}
\citation{bib8,bib9}
\citation{bib26,bib27,bib28,bib29,bib30,bib31,bib32,bib33,bib34,bib35,bib36,bib37,bib38,bib39,bib40,bib41,bib42,bib43,bib44,bib45,bib46,bib47,bib48,bib49,bib50,bib51,bib52,bib53,bib54,bib55,bib56,bib57,bib58,bib59,bib60,bib61,bib62,bib63,bib64,bib65,bib66,bib67,bib68,bib69,bib70,bib71,bib72,bib73,bib74,bib75,bib76,bib77,bib78,bib79,bib80,bib81,bib82,bib83,bib84,bib85}
\@writefile{lof}{\contentsline {figure}{\numberline {1.10}{\ignorespaces Common compliant devices. A binder clip, paper clips, backpack latch, lid eyelash curler, and nail clippers are shown.}}{5}{}\protected@file@percent }
\newlabel{fig:1.10}{{1.10}{5}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.11}{\ignorespaces Longbow in its unstrung, strung, and drawn positions.}}{5}{}\protected@file@percent }
\newlabel{fig:1.11}{{1.11}{5}}
\@writefile{toc}{\contentsline {section}{\numberline {1.3}HISTORICAL BACKGROUND}{5}{}\protected@file@percent }
\newlabel{sec:1.3}{{1.3}{5}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.12}{\ignorespaces Leonardo da Vinci's sketch of a compliant catapult. (From \cite  {bib22}.)}}{5}{}\protected@file@percent }
\newlabel{fig:1.12}{{1.12}{5}}
\citation{bib26}
\citation{bib81}
\citation{bib83}
\citation{bib81}
\citation{bib38}
\citation{bib58}
\citation{bib70}
\@writefile{lof}{\contentsline {figure}{\numberline {1.13}{\ignorespaces (a) Single-axis cross-flexure pivot, and (b) Bendix Corporation flexural pivot.}}{6}{}\protected@file@percent }
\newlabel{fig:1.13}{{1.13}{6}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.14}{\ignorespaces Load cell for force measurement.}}{6}{}\protected@file@percent }
\newlabel{fig:1.14}{{1.14}{6}}
\@writefile{toc}{\contentsline {section}{\numberline {1.4}COMPLIANT MECHANISMS AND NATURE\footnote {See \cite  {bib26}, \cite  {bib81}, and \cite  {bib83}.}}{6}{}\protected@file@percent }
\newlabel{sec:1.4}{{1.4}{6}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.15}{\ignorespaces Bee wings demonstrate the use of compliance in nature.}}{6}{}\protected@file@percent }
\newlabel{fig:1.15}{{1.15}{6}}
\citation{BIB38}
\citation{BIB58}
\citation{BIB70}
\@writefile{lof}{\contentsline {figure}{\numberline {1.16}{\ignorespaces An eel uses its compliance to swim.}}{7}{}\protected@file@percent }
\newlabel{fig:1.16}{{1.16}{7}}
\@writefile{toc}{\contentsline {section}{\numberline {1.5}NOMENCLATURE AND DIAGRAMS\footnote {The text and figures of this section are summarized from \cite  {bib38}, \cite  {bib58}, and \cite  {bib70}.}}{7}{}\protected@file@percent }
\newlabel{sec:1.5}{{1.5}{7}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.5.1}Compliant Mechanisms versus Compliant Structures}{7}{}\protected@file@percent }
\newlabel{subsec:1.5.1}{{1.5.1}{7}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.5.2}Nomenclature}{7}{}\protected@file@percent }
\newlabel{subsec:1.5.2}{{1.5.2}{7}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.17}{\ignorespaces (a) Compliant diving board, and (b) compliant cantilever beam.}}{8}{}\protected@file@percent }
\newlabel{fig:1.17}{{1.17}{8}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.18}{\ignorespaces One-link compliant mechanism.}}{8}{}\protected@file@percent }
\newlabel{fig:1.18}{{1.18}{8}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.19}{\ignorespaces Examples of link types.}}{8}{}\protected@file@percent }
\newlabel{fig:1.19}{{1.19}{8}}
\citation{bib86}
\@writefile{lof}{\contentsline {figure}{\numberline {1.20}{\ignorespaces Component characteristics of (a) segments, and (b) links.}}{9}{}\protected@file@percent }
\newlabel{fig:1.20}{{1.20}{9}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.5.3}Diagrams}{9}{}\protected@file@percent }
\newlabel{subsec:1.5.3}{{1.5.3}{9}}
\@writefile{toc}{\contentsline {section}{\numberline {1.6}COMPLIANT MEMS}{9}{}\protected@file@percent }
\newlabel{sec:1.6}{{1.6}{9}}
\citation{bib87}
\@writefile{lof}{\contentsline {figure}{\numberline {1.21}{\ignorespaces Symbol convention for compliant mechanism diagrams.}}{10}{}\protected@file@percent }
\newlabel{fig:1.21}{{1.21}{10}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.22}{\ignorespaces Diagrams representing the compliant mechanisms in (a) Figure 1.2\hbox {}a, (b) Figure 1.2\hbox {}b, (c) Figure 1.4\hbox {}a, and (d) Figure 1.11\hbox {}.}}{10}{}\protected@file@percent }
\newlabel{fig:1.22}{{1.22}{10}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.23}{\ignorespaces Scanning electron micrograph of a microcompliant bistable mechanism.}}{11}{}\protected@file@percent }
\newlabel{fig:1.23}{{1.23}{11}}
\@writefile{lof}{\contentsline {figure}{\numberline {P1.1}{\ignorespaces (a) Compliant member in a microengine, and (b) microengine that uses several compliant members. (Courtesy of Sandia National Laboratories, www.sandia.gov.)}}{11}{}\protected@file@percent }
\newlabel{fig:1.24}{{P1.1}{11}}
\newlabel{prb:1.1}{{1.1}{11}}
\newlabel{prb:1.2}{{1.2}{11}}
\newlabel{prb:1.3}{{1.3}{11}}
\newlabel{prb:1.4}{{1.4}{11}}
\newlabel{prb:1.5}{{1.5}{11}}
\newlabel{prb:1.6}{{1.6}{11}}
\@writefile{lof}{\contentsline {figure}{\numberline {P1.2}{\ignorespaces Figure for Problem 1.4\hbox {}.}}{11}{}\protected@file@percent }
\newlabel{prbfig:P1.4}{{P1.2}{11}}
\@writefile{lof}{\contentsline {figure}{\numberline {P1.3}{\ignorespaces Figure for Problem 1.5\hbox {}.}}{12}{}\protected@file@percent }
\newlabel{prbfig:P1.5}{{P1.3}{12}}
\@writefile{lof}{\contentsline {figure}{\numberline {P1.4}{\ignorespaces Figure for Problem 1.6\hbox {}.}}{12}{}\protected@file@percent }
\newlabel{prbfig:P1.6}{{P1.4}{12}}
\newlabel{prb:1.7}{{1.7}{12}}
\newlabel{prb:1.8}{{1.8}{12}}
\@writefile{lof}{\contentsline {figure}{\numberline {P1.5}{\ignorespaces Figure for Problem 1.7\hbox {}.}}{12}{}\protected@file@percent }
\newlabel{prbfig:P1.7}{{P1.5}{12}}
\@writefile{lof}{\contentsline {figure}{\numberline {P1.6}{\ignorespaces Figure for Problem 1.8\hbox {}.}}{13}{}\protected@file@percent }
\newlabel{prbfig:P1.8}{{P1.6}{13}}
\@setckpt{c01}{
\setcounter{page}{14}
\setcounter{equation}{0}
\setcounter{enumi}{8}
\setcounter{enumii}{0}
\setcounter{enumiii}{0}
\setcounter{enumiv}{0}
\setcounter{footnote}{3}
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
\setcounter{chapter}{1}
\setcounter{section}{6}
\setcounter{subsection}{0}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
\setcounter{figure}{6}
\setcounter{table}{0}
\setcounter{LT@tables}{1}
\setcounter{LT@chunks}{2}
\setcounter{parentequation}{0}
}

Another update: First off, you all are awesome. I've learned a lot from working through this, and your suggestions have helped me learn how to share more useful and general information here. So thank you.

I'm including three files: the main.tex, the referenced chapter c01.tex (which has isolated as little code as I can to provide a working example), and a .bib file with only bib38. It produces what I believe is the root cause of the error. Interestingly, if you comment out certain portions, it works great. Not really sure why.

main.tex file

\documentclass[a4paper,fleqn]{book}%

\usepackage[numbers]{natbib}
\bibliographystyle{unsrtnat}

\begin{document}%

\pagenumbering{roman}
\setcounter{page}{1}%
\pagenumbering{arabic}
\include{c01}

\appendix
\bibliography{zzbib}
% \include{b01}


\end{document}

c01.tex

\chapter{INTRODUCTION}\label{chap:1}



\begin{figure}
%\includegraphic{c01f011.eps}
\caption{Longbow in its unstrung, strung, and drawn positions.\label{fig:1.11}}
\end{figure}
\begin{figure}
%\includegraphic{c01f012.eps}
\caption{Leonardo da Vinci's sketch of a compliant catapult. (From \cite{bib22}.)\label{fig:1.12}}
\end{figure}

Flexible elements have also been used extensively in measurement instruments \cite{bib8,bib9}. Examples include high-accuracy load cells (Figure \ref{fig:1.14}) for force measurement, and Bourdon tubes for pressure measurement.

The number of products that rely on flexible members to perform their functions has increased significantly over the last few decades, thanks in part to the development of stronger and more reliable materials. The use of compliant mechanisms will probably continue to increase with time as materials and design methodologies are improved. The demand for increased product quality and decreased cost also pressures manufacturers to implement compliant mechanisms.

\begin{figure}
%\includegraphic{c01f013.eps}
\caption{(a) Single-axis cross-flexure pivot, and (b) Bendix Corporation flexural pivot.\label{fig:1.13}}
\end{figure}
\begin{figure}
%\includegraphic{c01f014.eps}
\caption{Load cell for force measurement.\label{fig:1.14}}
\end{figure}

University and industry research has played an important role in the development of compliant mechanism theory and application \cite{bib26,bib38,bib58,bib70,bib81,bib83}. Appendix \ref{app:A} lists a number of important publications in the area.

\renewcommand\@makefntext{}\def\thefootnote{*}
\section{COMPLIANT MECHANISMS AND NATURE\protect\footnote{See \cite{bib26}, \cite{bib81}, and \cite{bib83}.}}\label{sec:1.4}

Humans and nature often have differing philosophies on mechanical design. Stiff structures are usually preferred by humans because for many, stiffness means strength. Devices that must be capable of motion are constructed of multiple stiff structures assembled in such a manner as to allow motion (e.g., door hinges, linkages, and roller bearings). However, stiffness and strength cannot be equated--stiffness is a measure of how much something deflects under load, whereas strength is how much load can be endured before failure. Despite human tendencies, it is possible to make things that are flexible \textit{and} strong. Nature uses stiff structures where needed--tree trunks, bones, teeth, and claws--but in living organisms, it more often relies on flexibility in living organisms. Bee wings (Figure \ref{fig:1.15}), bird wings, tree branches, leaf stems, fish (Figure \ref{fig:1.16}), and single-celled organisms are only a few examples of creations that use compliance to their advantage. Nature also has the advantage of \textit{growing} living things, and no assembly is required \cite{bib81}.

\begin{figure}
%\includegraphic{c01f015.eps}
\caption{Bee wings demonstrate the use of compliance in nature.\label{fig:1.15}}
\end{figure}


\renewcommand\@makefntext{}\def\thefootnote{*}
\section{NOMENCLATURE AND DIAGRAMS\protect\footnote{The text and figures of this section are summarized from \cite{bib38}, \cite{bib58}, and \cite{bib70}.}}\label{sec:1.5}

zzbib.tex

@article{bib38,
author = {Her, I. and Midha, A.},
journal = {Journal of Mechanisms, Transmissions, and Automation in Design},
number = {3},
pages = {348-355},
title = {A Compliance Number Concept for Compliant Mechanisms, and Type Synthesis},
volume = {109},
year = {1987},
unidentified = {Trans. ASME},
}

Answer 1

You have provided very little information but I would guess you have something like

\documentclass{book}

\begin{document}

\chapter{aaa\cite{bib2}}

\bibliography{bib}
\bibliographystyle{plain}

\end{document}

With a current LaTeX this will work as you expected, producing

However if you have a old LaTeX you will get a warning

LaTeX Warning: Citation `BIB2' on page 2 undefined on input line 1.

as the \MakeUppercase used to make the uppercase page heading uppercases \cite{bib2} to \cite{BIB2}

\MakeUppercase in current LaTeX skips over \cite but if updating your latex is inconvenient you can add

\usepackage[overload]{textcase}

To define MakeUppercase in similar way

Or possibly better even with current LaTeX is to use

\chapter[short aaa]{aaa\cite{bib2}}

so a short form chapter title without the citation is used in tables of contents and page headings

---

UPDATED EXAMPLE

---

With the example added in the question later it is as guessed above, specifically you have

\section{NOMENCLATURE AND DIAGRAMS\protect\footnote{The text and figures of this section are summarized from \cite{bib38}, \cite{bib58}, and \cite{bib70}.}}\label{sec:1.5}

which makes, as well as the section heading on page 2, an uppercased page head on page 3 with (with an old latex) broken uppercased citations.

Use

\section[NOMENCLATURE AND DIAGRAMS]
        {NOMENCLATURE AND DIAGRAMS\protect\footnote{The text and figures of this section are summarized from \cite{bib38}, \cite{bib58}, and \cite{bib70}.}}\label{sec:1.5}

so the footnote does not appear in duplicated text