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It is almost definitely not a problem with calibre.
However, I know that calibre interfaces with a database on the Kobo. Not knowing much about Kobos (I am more of a Kindle person), I can only guess, but it is possible the database got corrupted. The usual advice for a corrupted Kobo database is to log out on the Kobo and then sign back into your account.
That will, I believe, require re-processing all the books on the device.
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