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did you delete any folders from the actual kobo itself?
there were a couple of empty folders left on mine from books i removed so i deleted those folders then got errors with calibre that it couldn't communicate with my device. i couldn't add or delete books, i tried a bunch of different things, then i just went to the home menu and did a factory reset and everything plays nice now.
luckily though i was only reading 1 book and had 10 loaded on there so it wasn't too much of a problem getting it back on.
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