The corrupted database error has to be fixed with a new database (either sign out of the account on the device, or a factory reset) or restoring a backup. If the corruption happens immediately after a factory reset, then something else is going on.
A likely reason is the internal SD card in the device is failing. If it is, then any update to the card could fail and be lost. That sounds like what is happening. But, you should also check what happens when you don't use calibre.
If you connect the device to Windows, does it show the device properly? Does it get mounted as a drive? Can copy a book to the device manually? When you eject the device, does it get processed an appear in the library on the device? Is it still there after restarting the device?
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