That as a solution has been discussed before in the Kobo forum. But, it does have a problem. By deleting the shelves and syncing, there is no message going back to the Kobo server make sure the duplicates are removed. Whether that is needed depends on exactly what happened on the server to cause the duplicates to be sent down.
Also, there is an easier way to do this. My Kobo Utilities plugin has a function to clean up the duplicates.
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