Thanks for your help Denis,
I think I'm starting to get a grasp on how this is working. 

If I run my document through the zotero-better-bibtex filter, then the 
docx+citations reader. I get some markdown like this:

---
...
references:
- 
...
  citation-key: Aigrain2021
...
  id: 476
---

# Introduction

Here is a reference to one of the entries in my bibliography [@476].

# References {#references .unnumbered}

It seems the zotero/better-bibtex filter is using an internal id (476) 
instead of the original citation key. I presume this is required for the 
integration between Zotero and Word.
I might try and dig in to the docx to markdown conversion to:

   1. Switch the ids of the citations back to the original citation key 
   strings.
   2. Consider exporting the 'references' metadata as a separate .bib file 
   instead of in the header.
   
On Wednesday, November 8, 2023 at 2:33:30 AM UTC+11 denis...@unibe.ch wrote:

> Pandoc will resolve citations when converting to docx. Your « -t 
> docx+citations » seems to have no effect here.
>
>  
>
> However, there exists a filter that might be useful here: 
> https://retorque.re/zotero-better-bibtex/exporting/pandoc/index.html#from-markdown-to-zotero-live-citations
>
> This will enable you to convert markdown citations to Zotero fields. 
> Obviously, this means you’ll need to manage your references with Zotero.
>
> Converting them back to Markdown citations should work out of the box 
> since 2.18, see the changelog : 
> https://pandoc.org/releases.html#pandoc-2.18-2022-04-04 
>
> Docx reader:
>
>    - Enable citations extension for docx reader (#7840 
>    <https://github.com/jgm/pandoc/issues/7840>). When enabled, Zotero, 
>    Mendeley, and EndNote citations embedded in a docx are parsed as native 
>    pandoc citations. (When disabled, the generated citation text and 
>    bibliography are passed through as regular text.) The bibliography 
>    generated by the plugin is suppressed. Instead, bibliographic data embedded 
>    in citation items is added to the references metadata field so that it 
>    can be used with --citeproc.
>
> So, here you’ll also see what the citations extension does for docx…
>
>  
>
> Best,
>
> Denis
>
>  
>
> *Von:* pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> *Im 
> Auftrag von *Alex
> *Gesendet:* Dienstag, 7. November 2023 10:03
> *An:* pandoc-discuss <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
> *Betreff:* Preserving citations between docx and markdown conversions
>
>  
>
> Sie erhalten nicht oft eine E-Mail von ac.ri...-Re5JQEeQqe9fmgfxC/sS/w@public.gmane.org Erfahren Sie, 
> warum dies wichtig ist <https://aka.ms/LearnAboutSenderIdentification>
>
> Hello! I am investigating using pandoc for my academic writing. I intend 
> to do the majority of the writing in markdown but will have others 
> reviewing and giving feedback through word (docx), and would like a way to 
> re-integrate the edits back to markdown while keeping the text as close as 
> possible. (md -> docx -> md)
>
>  
>
> In my markdown I have citations using the [@citekey] format:
>
>  
>
> Here is a reference to one of the entries in my bibliography 
> [@Aigrain2021].
>
>  
>
> I would like a way to preserve citations when converting between docx and 
> md.
>
> I've tried the following approach but just get plain text (in the 
> markdown) where the citation was.
>
>  
>
> Here is a reference to one of the entries in my bibliography (Aigrain
> 2021).
>
>  
>
> I am not sure whether the citations are being lost in the md to docx step 
> or the docx to md step. (I am not familiar with the how word even stores 
> citations)
>
>  
>
> Is what I want to do supported?
>
> I have the files:
>
> main.md
>
> main.bib
>
> nature-conservation.csl
>
>  
>
> The command I'm using to convert to docx (md -> docx):
>
> pandoc --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t docx+citations -o main.docx \
> -f markdown+citations main.md
>
>  
>
> The command I'm using to convert back to markdown:
>
> pandoc -s --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t markdown+citations -o main.md \
> -f docx+citations main.docx
>
>  
>
> Any ideas would be much appreciated. Thanks!
>
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