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Kovid has said in the past that reading and updating tags in PDF files seems to be bit hit-and-miss! Maybe you are seeing an example of this happening?
Epub files should have the metadata embedded reliably as long as you have used either 'Polish Books' or the Modify ePub plugin to make sure it has been updated to agree with the Calibre metadata database. Doing a conversion or a 'Save to Disk' will also update the metadata in ePub files.
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