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factory reset and re-add the books through calibre.
sounds like you most likely took the usb out of the kobo without properly ejecting it from your pc.
kobo's databases are sensitive and you have to take care with them or you'll get the error above.
so ya, go into the kobo, factory reset, re-add your books, go to my computer on your pc and find the kobo reader, right click and eject it, then you'll be fine for future adding / deletion with calibre so long as you properly eject.
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