I encountered this problem, and I believe I fixed it last week with
commit ba59e544. If you are able to build from source, can you check to
see if that fixes the problem for you?

bdh <bdhamilton-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:

> Hello,
>
> This is an issue with a lot of history, I'm seeing, but since everything I
> can pull up seems to have been resolved some time ago, I'm posting it
> again. Apologies if I'm beating a dead horse.
>
> Whenever I produce a docx file with footnotes using a custom reference.docx
> file, the resulting document announces it's corrupted when I open it. Word
> is able to correct and open the file anyway, but only after giving me a
> warning that says: "One or more footnotes references in the document are
> missing or corrupt."
>
> This occurs even simplifying things as far as I'm able:
>
> * Create a file `test.txt` with the content: `Test.^[Test.]`
> * Convert to docx *without *custom reference.docx in place. Resulting file
> opens fine.
> * Copy the resulting file into my pandoc directory with no changes, and
> rename it as `reference.docx`
> * Convert the same `test.txt` to docx, and the resulting file appears as
> corrupted.
>
> I'm using pandoc 1.13.2 on Mac OS 10.10.2, and Word for Mac 2011.
>
> This obviously isn't urgent, since Word corrects the error anyway, but I
> wanted to mention it.
>
> -- Brian
>
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