Thanks for your help. I found he solution through a Kobo rep. Because I've had the Kobo app on my iPhone and iPad and had previously made collections on it, those were automatically put on the Touch.
I deleted the apps on the other devices, factory reset the Touch and then I was able to modify and delete duplicate collections on the Touch. Then when I reinstalled the Kobo app on the iPad, the new collections were on it and all is well. Now when it does the sync everything works fine. I can make new collections on either the iPad or Touch and they'll appear on the other.
I really don't like the sync process on devices. To my mind they cause a lot of issues. The sync for my Sony readers drove me round the frigging bend!
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