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The Kobo Utilities plugin has a way to get rid of the duplicate shelves. The function is "Fix duplicate shelve" and is under the "Database" menu. This will display a list of all the shelves and the number of duplicates. You have a choice of keeping the oldest or newest (doesn't really matter) and whether to purge the entries from the database. Once you choose the options, press the "OK" button to get rid of the shelves.
If you don't choose the purge option, you should do a sync afterwards. This should tell the Kobo server to get rid of the duplicates. It generally works, but not always.
As a defence against this in the future, you can add an option the the config file on the device to prevent the shelves from syncing. To do this, you add "SyncShelves=false" into the "ApplicationPreferences" section of the file.
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