[QUOTE=Aylalake;2333234]The problem is that you CAN'T delete the shelves from the Touch! If I could, I would have done so. All that happens is that the books are deleted from the shelf (as well as the books on all the duplicated shelves) but the shelf itself cannot be deleted.
In Calibre double click the Kobo Touch plugin driver and select "delete empty shelves". Then sync the reader.