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can't you in theory just copy your ./documents folder (with all the .sdr folders) and then factory reset your kindle (or install the firmware new)? ..and then just copy the documents folder back?
the .sdr folders contain basically stuff like your current position in the book.. so if you copy them over and then back, it should still have all your locations in the books.
i don't know about the /var/local/cc.db, but that would be my first idea how to fix it the best.
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