Thanks for the advice. That's more of a last resort for me because I really don't want to delete my Ancestry tree. Ancestry is where I've done all the work and FTM was more of a backup. I'm too afraid that I'll lose information given all the sync errors FTM was giving me.
It's looking like my best bet in order to keep the tree is to go through and manually delete the copies of everyone. It'll be time consuming, but at least in the end it'll be right and I won't lose all my links and sources. I don't trust FTM to have synced them all properly, and I really don't want to have to upload ALL those images again (there are a lot of pictures on our tree!).
I guess what I was asking was, when syncing between the two, I know it will add new people to the un-updated tree, but will it also delete people that have been removed?
Auto-sync is definitely off. And will stay that way forever. In fact, I may never sync again once I get this fixed. I don't use FTM enough for it to be worth the trouble!