I currently don't have a tree with a sync issue but would like to understand your process in case a sync issue does show up.
When you say "I instead renamed the old sync file and forced FTM to upload a new copy to Ancestry (and link it). "
What steps did you take exactly to "force FTM to upload a new copy to Ancestry"? It sounds like that would result in a second AMT. Is that correct?
If so, does not the old AMT still think it is linked to FTM?