I gave in and did a factory reset today. Twice.
First, though, I renamed the shelves on my iPhone, in case they were the problem, by putting the number 1 at the end of the name. I then did a sync which created shelves with the same name (including the number 1) on my Kobo Touch. I still had all the dozens of duplicated shelves with their original names (without the number 1) which I could not delete off the Kobo Touch.
I put the iPhone in airplane mode to prevent any synching between the iPhone and the KT.
I then did the factory reset which cleared some of the duplicated shelves but not all. So I redid the reset and ended up with no shelves at all which is what I wanted.
After reloading my books via the Kobo Desktop, I then put the iPhone back to normal mode, and synched the KT and the iPhone.
I ended up with one shelf duplicated on my KT which did not have a 1 at the end of the name, so I checked my iPhone and sure enough, I'd missed renaming that one. I deleted it completely off my iPhone and was then able to delete it off my KT (a solution I was not able to use prior to the reset).
Interestingly, although the shelves created on the iPhone synced to the KT, the books ON the shelves on the iPhone didn't. So I ended up with empty shelves on the KT.
I managed to clear the duplicated shelves which was the point of the exercise. Now I will have to manually refill the shelves on the KT!
Bottom line - it looks as if it's a problem between the iPhone and the KT, and not anything to do with the KT software as such.
Last edited by Aylalake; 12-16-2012 at 02:52 PM.