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Hmm... I have the Kobo Utilities plugin, so I could get my reading positions back on those, and the covers aren't a huge issue, really... but I sideload absolutely everything through Calibre, so losing the collections would be a pain... and I'd be annoyed at the fact that everything was messed up in my book list(s) because I always have it set for me to see recent books at the top... I'd say something like 80% of the 8,000 or so 'books' on my Kobo are fanfiction, and I tend to read things I've added recently more often than I do older stuff, so having to try to remember a name of a fic or author and trying to hunt it down would be an issue.
I suppose if this is my only option I'll have to do it, but for the moment, if no one can think of anything I can do to fix the database, I think I might just tough it out. So far it's only been 2 books that have caused an issue, both fanfic. One downloaded with FanFicFare, and another made into a docx file and then converted to epub in Calibre by me. Calibre doesn't let me delete them, but I can delete them on the Kobo itself without a problem. And, oddly, I've been able to get the docx one to work after several delete and resend attempts... that's when the other story started glitching.
Anyway, thanks everyone so far for your suggestions, even if nothing has worked yet.
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