Well, it probably depends on:
how emotionally charged the matter is.
how much the other person, like wedrifid dislikes what they perceive as gratuitious complements.
You could also try an indirect complement, like "I knew you'd come around" or "Welcome to the club."
It's important to note that insulting a person for updating is relatively common but (always?) the wrong thing to do. An example from Stephen Covey:
One day a mother who was beside herself with anxiety called me. "My daughter is becoming interested in a [boy the mother was concerned about]. She is really becoming involved."
The more she talked, the more I was convinced that the problem was not so much with the daughter—it was with the mother. At every opportunity, she lectured that daughter and preached to her and used her boyfriend, who later became her fiance, as a weapon against her by saying, "Look at the kind of a boy he is. Do you want to marry a boy like that!"
"I love him."
I advised the mother, "Be careful you don't drive her into his arms. The more you deny her rights to be and to exist and to live, the more she'll feel to fight by behaving opposite to your expectations."
She could not understand this. Intellectually she could, but she was so subjectively involved that she could not risk another approach. She had never known another. Well, the girl and her fiance were married, and from all I heard, neither of them became very happy. The girl realizes what she has done now, and there is even a bigger gap because the parents tend to use her choices and problems as a weapon against her, saying, "We told you so."
Would it be supercilious to thank someone for updating? I know I would feel uncomfortable doing it, but I often feel the urge to do so anyway.
There seems to be something vicious about thanking them. My own estimation of my own belief has not changed in these situations. I feel fairly satisfied that the other has considered my view and has shakily come to agree with it. I worry it would be a little like saying 'screw your opinion, now you see I'm right.'
However:
It is both rational and polite to thank them. The gentlemen's agreement of rationality allows for one person to be wrong and not lose face at all. When someone concedes something to me (a point) I typically feel the need to thank them.
What do you think?