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This was a huge help! Constructing a hybrid database by moving the user table values worked great, my annotations are back. There's a little bit of glitchiness but nothing that interferes with my reading so far: a couple dozen 'new books' appeared with the name index by unknown author, composed of chunks from books I've read before. I suspect they're related to old annotations.
Deleting the table and using a CSV to hold the values ended up messing with the table settings (I don't think sqlitebrowser really understand the BIT field) but since there are less than a dozen values I ended up just editing the table with copy/paste. 100% fixed, I'm going to stay away from firmware updates in the future unless there's some stupendous new feature I can't live without.
Thanks again.
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