Just to tell you, Allison, that I've had experiences parallel to your's:
I recently downloaded and installed "the bonus update" for Family Tree Maker 2012. I then opened FTM and started synchronizing my offline and online family trees. The synchronization failed several times so I ended up with the "usual procedure" of first deleting my FTM tree and then downloading my Ancestry family tree to FTM. After working a bit with the FTM version, I synchronized again and every thing seemed to work fine. I then started working with my Ancestry tree. And horror! First thing that struck me was a lot of "media" in the media gallery without any actual pictures, but only a standard graphic symbol of media. Next that there endless duplicates of a lot of my source records, apparently the ones I've added the last half year or so. Finally I found out that also people were duplicated. But the duplicates were in fact not "endless". There were always 1 original plus 4 duplicates. Of course the duplicates also were to be found in my FTM tree because of the synchronization. But it's a lot easier to handle duplicates in FTM than in the Ancestry tree. But like you I don't want to waste my work through almost two years, with nearly 3000 people, 1345 photos, and many times more source records added. And the links, people invited to share. No! So instead I've spent many hours cleaning my tree, and I'm still not there!
Of course I contacted FMT support through email. But all what he did was to refer to the "Get Help"-procedures for deleting duplicates in FTM. And else convince me that it all happened because of some "user error"! When I referred to the fact that the duplicates came in a fixed number, proving to me that it had to be caused by a programmatic error, and asked him how I could contact Ancestry.com about that through email (no way that I'll make long distance phone calls from Denmark, discussing complicated technical issues in English, not being used to talk in that language!) he stopped communicating!
Until Ancestry convinces me that they have recognized and solved the problem I'll seriously warn against using the synchronizing feature. Instead I advise downloading one's online tree to FTM as a new tree at some interval.