% pandoc -f latex -t native
\begin{eqnarray}
A&=&B,\\
C&=&D,\\
%\end{eqnarray}
%\begin{eqnarray}
E&=&F
\end{eqnarray}
^D
[Para [Math DisplayMath "\\begin{aligned}\nA&=&B,\\\\\nC&=&D,\\\\\n%\\end{eqnarray}\n%\\begin{eqnarray}\nE&=&F\\end{aligned}"]]