I have stayed away from the sync functionality until a few weeks ago. I actually have never been an online tree fan. But I am helping someone and created a new file and
uploaded to Ancestry so she could see the progress. While I can't positively conclude the problem is through the synching vs. just FTM2012 or user error, I'm very suspicious. My main FTM file which has never been uploaded is just fine and I've been adding to that file for years vs. just a few weeks for the corrupted synced file.
See my series of messages for "Corrupt Source".