You can use the trick discussed here
Basically, Pandoc is coded to recognize \begin and \end, so instead define \Begin and \End in the header and use those.
E.g.:
---
papersize: a4
documentclass: article
header-includes:
- \usepackage{multicol}
- \newcommand{\hideFromPandoc}[1]{#1}
- \hideFromPandoc{
\let\Begin\begin
\let\End\end
}
...
H1
==============
H2 - A
--------------
\Begin{multicols}{2}
### H3 - a
Blah blah blah...
### H3 - b
Blah blah blah...
### H3 - c
Blah blah blah...
\End{multicols}
H2 - B
--------------
Blah blah blah...