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The Kobo firmware should never be holding files open when they are exposed over USB. If that is indeed the problem, then the solution is simple, Kobo needs to update their firmware to release the db when connected by USB.
You could work around the problem with the steps you describe, but the problem is that there needs to be an automated way to get the Kobo to close an re-open the db. Without that, users would have to remember to reboot the device on every disconnect which is not a workable solution. Probably the Desktop Application does something to force a db close/re-open. If you can figure out what, then the calibre driver could do the same.
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