Given all the sync problems, and what I've been reading on these boards, I've decided that while it will be a major pain in the rear, my best bet to have a clean online tree is to go through and manually delete the duplicates, rather than trusting another sync to fix them. I don't want to delete the online tree and re-upload because while I can re-invite the few people with access to it, there are quite a lot who have linked to people on it that will lose those links, not to mention the hours of time I've spent clearing hints that will be lost.
Aside from the fact that every sync I've done since May has had an error, I have a LOT of media, and since there is no way to tell FTM to sync without the media files, I don't feel like it's worth the amount of time it will take to sync them all, especially when the end result will almost definitely be an error with corrupted and/or duplicated files.
Thanks to everyone for their help. I've learned my lesson the hard way and will never sync FTM to Ancestry again. I'll go back to using it the way I used past versions and keep it as a secondary, manually-edited backup. Needless to say, I'm disappointed that I spent the money to upgrade from 2011 when all it did was create a problem that's taken nearly a month of my time to fix, and will likely take another month to get my online tree back in order.