Oh, no!! One thing I learned, is that by looking at the Sync Report carefully, if it shows that a bunch of people are to be added from FTM to Ancestry, or if it asks which file changes should be made (FTM or Ancestry), or if the wrong media file name is attached to multiple people, that is an indicator that the FTM tree is broken, corrupted or otherwise, messed up very badly.
I tried running a sync several times, stopped the timer and looked at the report carefully over the past few weeks. I wish I had figured out earlier what to look for.
Finally, today, I unlinked my tree that was having problems, and re-downloaded the tree from Ancestry before it sync could mess it up again.
I keep my main tree on Ancestry and backup on FTM. For those who do it the other way, they would look for different things than I do. I sent a bunch of stuff to support to send the developers; don't know if they did or not.
Ancestry support asked me to create a new tree and see if it fails. Of course, the smaller trees almost never fail to sync.. That exercise didn't show anything useful, other than that the program works well for syncing sometimes and sometimes, it doesn't.