I experienced many of the same issues with the sync feature. After syncing, I'd have multiples of people, life events, and records with the original formatting of dates changed in the duplicated events.
I stopped using FTM for my desktop program. When I got a new program (Legacy), I downloaded my messed up ACOM tree (GEDCOM) to try to fix it. The majority of the database has been corrected now but I still find a few problems from time to time.