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I have fixed the duplicate shelves problem. After deleting the shelves on the Glo using the user interface, I connected it to my computer via the USB, and I used SQLiteSpy to open the .kobo/KoboReader.sqlite database. This showed that the Shelf table still had 3 records in it which matched the shelves I had deleted. So I deleted these records, disconnected, reconnected, ran Calibre to resync the shelves, and I now have the correct number of shelves (3).
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