How many shelves do you have? There was a problem if you had a lot of shelves that syncing would hang like this. Or maybe it took so long I never waited it out. This has been fixed, but I'm not sure which firmware it is in.
If you want to try, you can add the line "SyncShelves=false" in the "ApplicationPreferences" section of the "Kobo eReader.conf" file. This prevents shelves from syncing, so would eliminate one possibility for the hang.
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