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I am trying to implement the lemma numbering solution in this question. I am currently compiling the document from a parent file such that:

\usepackage{chngcntr}
\usepackage{apptools}
\AtAppendix{\counterwithin{lemma}{section}}

\newtheorem{lemma}{Lemma}

\begin{appendices}
\include{Appendix1/appendix1}
\end{appendices}

where the appendix file has

\begin{lemma}
A lemma in appendix.
\end{lemma}

The lemma number remains sequential and doesn't change to reflect that it is in the appendix file...

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I added a line to this section of code

\begin{appendices}
\appendix
\include{Appendix1/appendix1}
\end{appendices}

Not sure if this is the correct solution, but it works.

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