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Just an update. I ended up having to log out and log back in and therefore rebuild the database (which I didn't want to do) but I at least found a quick fix for the books not being in the collections like I want. There's a table in the KoboReader database called ShelfContent. I was able to export that table from the corrupt database and import it into the new database (where it was blank) and everything appeared back on my shelves. The only downside is that nothing is in the order I want it even though the date is in that particular table.
If anyone knows of a way to get the books in the right order by date they were last accessed or even date they were originally uploaded, I'd be very appreciative.
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