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From my experience it could be related to the version of weasyprint and pydyf used by the plugin (more info on the issue #157 ).
But it could also be related to the mkdocs-with-pdf plugin configuration you used in mkdocs.yml or the plugin mkdocs-minify-plugin since it change the HTML after the site generation and that mkdocs-with-pdf make use of the HTML tags to find the content it need to render as PDF. Could try to use mkdocs-with-pdf with basic configuration and all others plugin disabled to see if it caused the problem.
I am trying to render the amazing https://books.japila.pl/spark-sql-internals/ as a single PDF, but the result contains only a subset of the https://github.com/japila-books/spark-sql-internals
document.pdf
also the sitemap is significantly larger than the pdf
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