It sounds a bit similar to the problem I have with my Aura. It seems to drop off the USB bus randomly. It connects fine, Calibre sees it, and I can send books to it. And then when I try to send another, Calibre errors out with 'The system can't find the file specified'.
At that point Windows (XP Pro 32bit) has lost the drive as well; the drive letter is still there, but I can't do anything with it anymore. Ejecting the device and reconnecting it fixes it most of the time. For a while.
The funny thing is that it never, as yet, has damaged either the file system or the Kobo database (both chkdsk and the Kobo Utilities plugin give it a clean bill of health afterwards).
Changing the USB port or cable doesn't make a difference, and neither has a factory reset. I haven't tried another PC yet.
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