With Pandoc3.6.4, equation labels are seemingly skipped.
For example,
% test.tex
\begin{equation}
\label{eq:U}
U = A
\end{equation}
after running
it gives
version specifics
pandoc 3.6.4
Features: +server +lua
Scripting engine: Lua 5.4
OS: Linux x64 6.5.0-21-generic