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This issue would be better asked in the Workshop forum, so I'm moving it there.
Calibre is just one of several tools/processes to get from a LatTex generated a PDF to ebook formats.
For personal use I would convert the LaTex output (.tex ?) to DOCX, then use Writer to edit/style the document, and then convert DOCX to flowable formats.
The professional bookmakers, who inhabit the Workshop forum and who are familiar with LaTex will undoubtedly have alternative ideas.
BR