No, FTM2 won't sync at all. I only get an error message as detailed in my first post.
I only started using the iPad app after a couple of days, before that there were no problems syncing between AMT and FTM2 at all. But now that I've been making changes via the iPad app, it won't synch.
The only way 'round it was to delete my FTM2 tree and "create new" using the "existing Ancestry tree" option to re-create the tree in FTM2. Fortunately I hadn't made many changes in FTM2 so I hadn't lost anything.