[JSWolf]

Originally Posted by Xylon

Interesting, thank you.

So to make the initial example a bit clearer:

1. my case for example I've copied books A, B, C, D and E to the ereader. All stats were set to unread automatically.
2. I then copied the sqlite file, which had information about A, B and C (D and E were added later and were not in this backup).
3. After copying the database, A, B and C now had the actual restored read status, D and E were no longer being shown.
4. I copied D and E back from Calibre to the ereader so that they would show up again, but then it'd optimize and also reset the status for A, B and C.

I've also just tried your other suggestion. I copied the sqlite database back to the device, it now shows the read progress on the ereader, and all the annotations.
However when I now try to store the bookmarks it says:

calibre, version 7.17.0
Kobo Utilities - Library updated: Update summary:
Reading locations updated=0
Books with no reading location=1
Total books checked=1

As if it just doesn't really fully recognize the database that was copied to it. At the same time, Calibre does show a checkmark before the books it finds.

Did you reboot after ejecting the Kobo from the compter?