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Did you connect over USB to verify that the books are still there? If so, it sounds like your database corrupted. You can restore a backup if you have one, or you can do a factory reset to wipe the database and start over.
What firmware are you using? 4.37 and 4.38 seem to both be prone to database corruptions compared to 4.35 and earlier. You may also wish to downgrade the firmware to see if that stops the problem from happening again.
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