No. It is too late now. If you call ancestry they will tell you this always the case. At this point you will need to decide which has better info. If you really want the stuff on your online tree you will need to download into a new FTM file. If your FTM is good/better then you will just have to live with the new arrangement and re-invite people.
It is possible not to end up with duplicate trees, But the preparation has to be done ahead. There are two ways: one is to backup FTM making sure to check all the sync boxes, and then restore that backup and sync SHOULD restore.
The other way is to save your documents folder on an external hard drive INCLUDING app data folder which is normally hidden. Move this folder to the "new" computer and then install FTM. This is what I did and FTM didn't even know it wasn't supposed to sync.