I am posting this in case my solution helps someone else. I work in both FTM and ancestry, and frequently make changes in both I use Tree Sync to keep them the same. I never really experienced sync errors until about four days ago. At that time, I had a failed sync when exiting FTM. Since it was the end of my night of research, I decided to look into it the next day.
When I restarted FTM the next day, the sync started and I received the familiar conflict resolution dialog. The conflicts were suprising though. These were people I had just added to my tree online prior to the failed to sync the previous night. I had never had them in FTM before. FTM actually had added them despite the failure notice. I decided to "resolve" the conflicts by accepting the Ancestry data overwrite the FTM data. The sync failed again. I retried the sync manually and this time the number of changes to people, sources and citations were double the previous number. I decided to abort this sync after recording the "conflicting" names.
Upon further investigation, I discovered that there were 2 entries for each person, 2 sources for each actual source, and 2 citations for each citation. I cleaned these up by manually removing them from FTM and tried to resync. Again, I was forced into coinflict resolution. Again I attempted to resolve and sync, and again it failed. Upon investigation, I had again created entries in FTM for each person, source and citation despite the failure notice. I retried the sync and samw the same conflict resolution scenario and it again doubled the entries. I decided that I would break my link and delete my online tree, clean up the file and try to upload again.
After all of this work, my upload/link failed. After much digging, I found that they were failing because I had about 90 citations that were not linked to a source anymore, but were all linked to people. All of these were citations created by utilizing census hints on ancestry, so they obviously were not created unlinked this way be me. I manually linked these citations back to the proper source records, and behold, I was able to upload and link my tree again.
I never did figure out why the tree-sync was failing, but it might have had something to do with those unlinked citations. I plan to keep good regular (daily) backups now.
I have not called Ancestry tech support yet, but I plan to do so and will try to post the results here.