Having two trees on ancestry (or two trees in ftm) is an expected result of starting the sync process since ftm cannot sync (the first time) to an already existing family tree. You have a choice of leaving your old tree up (public or private) or taking it down. If everything you wanted did not get transferred you might try using member connect to get stuff from old tree to new tree. Most everything except comments should have transferred though. And yes, you will have to re-invite people. I kept my old tree up use it for experiments and marked it private.