If Pandoc doesn't natively support this scenario, you might consider writing a filter to extract and remove the sidenotes into a separate file/location and write an additional program manipulating the docx Open XML or the Word application object model to merge the sidenotes back in.

On Tuesday, September 15, 2020 at 11:41:58 PM UTC+3 Denis Maier wrote:
Am 13.09.2020 um 21:44 schrieb Leonard Rosenthol:
> Looks like you can -
> https://wordribbon.tips.net/T010668_Adding_Sidebars.html
>
> You can also do text boxes, pull quotes, etc.   However, I didn't dig
> into which coudl be done with custom styles and which would require a
> (Lua) filter.  But the features are there in DocX if we figure out the
> best way to expose them...

Well, maybe... but, the link above is about Sidebars, which I understand
as adding arbitray content in the margins. That's not the same thing as
sidenotes, maybe a visual approximation, but I think there won't be any
link between those boxes and the text. There even won't be a note number
in the text unless we add one. And the worst part might be placing those
boxes in the margins. There are some LaTeX packages that go at great
lengths to keep the sidenotes close to the calling location, but also
move them around if need arise, e.g. when the note is called near the
end of a page, or if there are to many notes. (Does pandoc even have
access to these details?)

Anyway, all that doesn't fundamentally speak against implementing this.

Just one remark regarding this particular case: The OP wrote he is going
to send his manuscript to his publisher. So I guess the publisher will
do the layout anyway, and I doubt that the typesetter will appreciate a
docx with notes in the margins. (At least I wouldn't.)

Best,
Denis

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