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Unfortunately the damage is probably already done regardless of any access being done by calibre to the file system.
The presence of any of the wal / shm files means that processes have not been shutdown cleanly on the Linux side of the Kobo, before the file system has been shared via usb with the PC. I don't recall all the details but it's even possible that the shared file system has been remounted as read only on the Kobo side.
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