The latest advice I have had from Ancestry Support, is to upload my tree to Ancestry, using FMT 2012, then unlink the tree, then download the tree from Ancestry using FMT 2014. This I did last night and took about 3 hours. The media files were the ones that took the longest.
I now have my tree in FMT 2014. The index of people are the same and info looks ok so far.
But there are still problems, as FMT 2014 is telling me to Register and activate Ancestry, but it will not let me. So another phone call to Ancestry Support is needed.