From the information given, I think that the AST must still contain a fig:fig1 citation after your filter has run. Are you able to share your filter?

On Wed, 29 Nov 2023 at 13:28, 'Thomas J.' via pandoc-discuss <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
Hi everyone,

Since pandoc-fignos isn't working anymore (at least, with my Pandoc version), I have written a Lua filter that basically does what fignos does, namely replacing tags such as @fig:fig1 with anchors/refs to the figures in html/latex. Now, if I am trying to use this filter without citeproc, everthing works as expected. The moment I use --citeproc, I get the error message "fig:fig1 citation not found" and I have no link in my output file. I am actually calling the lua filter BEFORE --citeproc in the command line... 

pandoc --lua-filter=filter/pandoc-figref.lua --citeproc --number-sections --from markdown --template=templates/phimisci-1-5.html --bibliography=$BIBLIOGRAPHY --csl=csl/apa7-single-spaced.csl yaml/gen-metadata.yaml article/$1 article/$2 -o $HTMLFILE

What am I missing? Thanks for the help!

Best wishes,
Thomas

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