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Unfortunately things like crashes can cause problems.
The database is located on the portion of the internal SD card that is shared with the PC. Before the database can be opened on the PC side it has to be fully closed by all processes on the Kobo side. There was a long standing issue in the 4.x code (and I don't remember which version fixed it) where the database was not closed on the Kobo side when the storage was shared to the PC.
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