Do you actually want to sync the two trees, on family tree maker and on ancestry?
You would then follow the steps here:http://ancestry.custhelp.com/app/answers/detail/a_id/5360
I think at the end you are given a choice whether you want to keep the link of the file you just downloaded, or just have it as a separate downloaded file.
Syncing is good, I like it. Not everyone does. It will keep your tree up to date in both places.
But first, after you first do this you will have two trees essentially the same on your FTM. If you are sure the tree has what you want you can just delete your old one.
You can also merge the two trees in FTM but you have to have a lot of patience and a lot of computer memory to do it.
From what you said, it sounds like you just want to check and then delete the old tree [well, don't delete it.. you may want to keep it around.. but as an "old" tree.