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Thanks for the response.
I am able to open and read the PDF files. One of them was not editable in FOXIT, so I set it to allow, which allowed the Calibre embed to work. The other was fine and readable, and passed a QPDF check. I was able to edit the metadata with Stirling PDF. So, not knowing what was happening I used ghostscript to rebuild it, then it worked with Calibre.
Both of these were part of a group of 10 PDFs that I selected, after the failure the log only showed the first failure, not both. Next time I will open each PDF in the list and check if the embed feature continued to write the remaining files. One thing I noticed is that the embed is only appending authors not overwriting them. So, a PDF with lastname, firstname would end up being "firstname lastname; lastname, firstname" after the embed.
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