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The images referenced by notes need to be IN the documents, not referenced by a file path or local webserver. It's accidental that it ever worked.
Also Calibre is good for ebooks, PDFs are not real ebooks, other tools work far better to create a PDF, such as LO Writer with built-in PDF generation. Years ago I used Word 2002 with a PDF plug-in and it also generated perfect PDFs.
While i use Calibre all the time to create and manage epub, mobi, azw3, pdb, lrf etc and export RTF from badly formatted PD ebooks, I'd never use it to create PDFs. Only to catalogue smaller page size ones that can be read on the eink based ereaders. I don't use Calibre to catalogue or manage larger format PDFs (old magazines, service manuals, datasheets etc) but organise them by directory and function and copy to the 10" tablet.
So I'd only use Word or Writer to do what you are doing and I'd make sure the document included ALL the files, no paths or links outside the document to webservers or files even if local. Don't use Calibre at all for this.
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