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I may have the same problem. The issue for me is that the calibre doesn't list all the books on the "Device" window, so I can't manually match the books, and some books are only on my kobo, but not in my calibre database, but this should not matter (or maybe it does?), calibre still should see all the books on kobo.
And just deleting books from kobo and reuploading won't work, because all new uploaded books won't appear on "Device" window when you reconnect kobo.
This problem occurs to me a second time. Both times after I used fresh calibre installation with a new database (the books were uploaded with my previous calibre installation), I did not bother with backups as I don't have that many books or a proper database, I just add a book to calibre and upload to my kobo as I need. I could not figure it out the first time so I just reset my kobo and that fixed the problem, but this is not ideal solution.
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