\makeatletter
\makeatother


So my body is:

\input{discussion/discussion}

\appendix
\begin{appendices}
\makeatletter
\makeatother
\input{appendix/walking-statistics}
\input{appendix/standing-statistics}
\end{appendices}

\bibliographystyle{alpha}
\bibliography{bibliography/HRG}


This results in a TOC like:

5  Chapter
5.1  Section 1
5.2  Section 2
Appendices
A  Lorem Ipsum
B  Lorem Ipsum II
Bibliography


5  Chapter
5.1  Section 1
5.2  Section 2
Appendices
A  Lorem Ipsum
B  Lorem Ipsum II
Bibliography


But I can't figure out how to essentially "undo" the change in the way that chapters are organized in the table of contents.

Change the \addtocontents command to
\addtocontents{toc}{\bgroup\let\protect\l@chapter\protect\l@section}

and add the following line at the end of your appendices environment:
\addtocontents{toc}{\egroup}

This delimits the effect of the \let statement to the area between \bgroup and \egroup.