I have reported this to support and stayed on the phone with them as they recreated it themselves. Two new updates for FTM 2012 have been released since then. You should document your finding and report it too so this get fixed.
PS. Read the forum here for a way to back up your synchronized tree in the future so in the event of a broken TreeSync you can restore manually without starting anew. Since you cannot merge your backup with a newly downloaded tree from AMT without causing duplicates, this is your only way to avoid losing work.
PS. Read the forum here for a way to back up your synchronized tree in the future so in the event of a broken TreeSync you can restore manually without starting anew. Since you cannot merge your backup with a newly downloaded tree from AMT without causing duplicates, this is your only way to avoid losing work.