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Originally Posted by Amon_Re
Can confirm it also happens with Calibre & Fedora Linux, it's not limited to windows and must be something on the Kobo itself that f's up.
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Given that the failure to close the database which would flush the .sqlite-wal and .sqlite-shm files must occur before the USB connection, you are correct that it is an issue on the Kobo. In my testing, it happened on MacOS Sonoma, Windows 11 x64 and SUSE Tumbleweed.
I have also found that forcing a reboot before connecting to the computer keeps the issue from showing up for me.