I finally bit the bullet and unlinked my file on Ancestry. I then created a new file on Ancestry and synced to it. I really hate doing this because I think it screws their indexes all up. Now when somebody tries to reference something they find from my tree, it will give them an error that it is no longer available. At least until they re-index.
I also find it weird that it wouldn't sync and now it does with no change to my file on FTMM2. The problem is apparently on the Ancestry side.