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There are several things that could cause this.
A couple of updates past, Calibre "broke" the Kobo Db. It has been fixed now, but folks have had to reset to factory default, or replace the sqlite and image files (see the sticky above).
Some folks have reported that their security software was not letting the desktop communicate and sync.
There have been some instances of the update to the new desktop software was pooched. The solution to that seems to be to uninstall the software. Reboot. Install it again.
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