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You could try the "Optimize Database" item right under the configuration item for updating. I suspect that there is a bad entry in the database, perhaps from an ebook that is causing problems for the scanner. If you can remember which books were added just before the problem showed up, you could try removing them to see if it clears up the problem. If so, add them back one or a few at a time to see which one causes the problem. Use the library app to delete books, since that also updates the database as it does so.
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