I have been getting this error (AGAIN!) for the last couple of days. My tree is backed-up and compacted and whatever else has been suggested in this thread. I had the same thing happen in December 2012 and it was a mess! Somehow, during an attempt to sync, two of my trees merged together! I finally had to rebuild my tree and upload it again to ancestry, then reinvite everyone who had permission to view my tree on ancestry. Now I am nervous that something else will screw things up with my online tree. Yes, I can always upload it again from a backup but this will make the fourth time I've done this and it's majorly aggravating. For the money I spend every year on my ancestry subscription and for software, I expect things to work much, much better!!!
I agree with Daniel Reese...it would be reassuring to hear some kind of feedback from ancestry regarding this thread and our problems.