I believe there have been some minor bugs in the sync code that has altered some of my data for media files, and I have also noticed some changes to relationships. I honestly have reacted to this by sort of putting my head in the sand and hoping that it doesn't happen again (though I have reported the errors to the FTM crew).
I've noticed errors with my media files the most. The most common one is a failure to sync a change to a caption. The next most common is the description for one media item being written over an existing description for a different media item.