Kobo syncs books and information between devices and apps logged into the same account. The books synced are only the kepubs. The information synced are things like reading stated (finished, current position), bookmarks and annotations and shelves and the kepubs on them. Generally, this works well.
Unfortunately, Kobo have a problem on their server at the moment. The shelves are being messed up. I did a factory reset of my Touch today and connected to the PC and ran the desktop app to update to the latest firmware. When this finished I had 249 pages of shelves. A lot of them were repeats. When I synced my Glo, it also got all these shelves.
I had a look into database and found that all shelves I had created and deleted since July had come back. I believe that part of the issue is different versions of the database and shelf handling code on different devices. The Touch went back to an earlier firmware version during the update and I think that caused or at least made the problem worse.
The solution to this problem for me was to update the shelf data in the database and then do a sync. When I synced the other device, the shelves on it were fixed as well.
The shelf problem is not caused in anyway by calibre or the driver. The reason for the factory reset above was to do some testing for Kobo and I made sure that calibre didn't go near the device. The idea was to prove it was the device or software and in no way was it calibre and the driver.
Also, I have sent you a PM about some more information for the original problem.
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