kobotux: The error tells me the database on the device is corrupt. Losing book or reading status is a common sign of this. This usually happens when you power the device off and on. As you say it happens after hours of sleep, I suspect you have the device set to power off after a period of sleep.
The fix is to either restore a backup of the database, or to signout of the Kobo account on the device. This will replace the database with an empty database, restart the device and take you through the basic setup. Then all the sideloaded books will be reloaded. Unfortunately the reading status of these books will be lost, but it will solve the existing problems.
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