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I may be wrong but I thought calibre used the folder ID to recognize books. This should not change unless you change the author and/or possibly title.
You could resend the books although this might reset your reading place and bookmarks.
Just a shot in the dark, but do you have automatic management turned off? Mine is on. My books seem to be still recognized after metadata changes, conversions etc. Without resending. I don't have any Paper books entered though.
Helen
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