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I have had the same problem with my Clara, so I started doing database backups with Kobo Utilities plugin. Then when it happened, I would just copy the backup db to the Clara, reboot and it was fine. It works, but it seemed kind of messy to me.
Anyway, in one of the last firmware update threads, the corruption was happening to more people. Someone observed that it usually happened when connecting with a book open, but not when you go back to the home screen or books page. Since then, I've made a point of making sure I did that and haven't had the problem anymore.
I only have epubs, so maybe it's a problem with them and not kepubs? IDK but it works for me so far, might be worth a try or at least do backups.
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