Hmm. When this happened to me just now, I didn't read this first. So my trees are now unlinked, and I then re-upload from FTM to ATM.
Which means that I now have TWO copies of my tree on ATM, one linked and one not, with all of my invites on the old tree and no invites on the new tree.
Is it safe to delete the old one, so that I only keep the linked tree, or is it only living in one place but with two names? I don't want to lose everything! (Needless to say, I have just backed everything up!)