The same problem happens with latex output only if you don't pass to pandoc the command line --chapter Obvious, because footnote numbering restarts each chapter and not every section.
The solution seems to insert in the DOCX file a "Section Break (continuous)" before each Level 1 header and set "number footnotes per section". This second setting could be obviated with a template document, but the first one no because the break is not part of the heading. Is it possible to add an option to pandoc to add (in the DOCX writer) the section break before each level 1 header? One possible way is to overload the --chapter option to work in DOCX writer adding the break. Thanks! mario

I know this is an old issue but I was wondering if this has been solved in the meanwhile. I have tried changing the setting to "number footnotes per section" in the docx template document I'm using but it does not solve the problem. I have also tried applying a filter creating section bibliographies (https://github.com/pandoc-ext/section-bibliographies). That does what it says but does not restart footnote numbering as hoped for.

Is it possible to add an option to pandoc to add (in the DOCX writer) the section break before each level 1 header?

You could probably use a Lua filter to do this. (Adding RawBlock element with format openxml; but you need to get the XML exactly right.)

Is it possible to add an option to pandoc to add (in the DOCX writer) the section break before each level 1 header? One possible way is to overload the --chapter option to work in DOCX writer adding the break.

This is not a bad idea.