I see two options... one going back to a previous backup, which would involve starting over and having two trees either online or on your computer, or the other just correcting the tree as it stands as you seem to be able to do. I was going to say happy, but that didn't seem exactly the right word.
Going forward, you should keep several backup copies of your tree, and even keep some of them OFF of your computer and even OUT of your house, for real security. These need to be made using file/backup or some other means of backup, not counting on the automatic backup that FTM does.
Probably you were OK in the first place with the extra tree on Ancestry since a new sync after the link is broken always makes a new tree in either one place OR the other, not both. That tree is probably the one you should have kept.
Now that you have a tree on Ancestry and a tree on your computer though I'd tend to leave as is. Look at the list of ALL the people in your tree and see if you have any duplicates, then merge them. I'd do the merging in FTM I think as it tends to bring along families better.
But keep syncing. Like after every single change that you make. Make one change in FTM. compact the file. [more than once if needed]. Then sync. Then check both trees. Repeat.
Anyway, those are my thoughts.