I suspect the common markdown workflow is to merge and track changes as one 
does with software source code, and not via Word. But I'm a software 
developer so I might be biased. More specifically, this workflow is to keep 
the markdown as the source-of-truth, use version control software like git, 
and merge each and every change back into the markdown as soon as possible 
(with git) and not after an extended period of changes managed by Word.

Halie Rando might have some advice and this thread might be of interest 
(you can find their contact info via the thread and github):

https://github.com/manubot/rootstock/issues/226

Sorry I don't have an easy solution to share. Overall it sounds like a bad 
situation you've gotten yourself into, sorry to say.
On Thursday, January 12, 2023 at 6:12:28 AM UTC-5 the.so...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:

> Dear all,
> Recently, I wrote a paper with extensive citations (more than a
> hundred footnotes) in Pandoc-flavoured Markdown, using Zotero for
> reference management and an exported CSL YAML file.
>
> To interact with the reviewers and copy-editors, I had to produce a
> DOCX version. They added comments, and suggested changes via tracked
> changes. I accepted many of the changes suggested, rejected some, and
> made various other changes. I now have a final DOCX version.
>
> From that final DOCX version, I would like to produce:
> 1. a final Mardown version
> 2. a diff between my draft Markdown version and the final Markdown version
> 3. a publishable PDF version using pandoc (rather than LibreOffice)
>
> I can generate a Markdown file from the final DOCX version, but that
> doesn't preserve the original Markdown citations as @-citations, but
> renders them as text footnotes.
>
> I'm sure it's a common workflow, so how do other people deal with this?
>
> Regards,
> Pranesh
>

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