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?
I would find it mildly patronising but would not be offended.
I would prefer to be thanked for taking the time and effort to engage with you, understand your perspective or position and have a positive human interaction. If I am also willing to signal that I have changed my mind based on your words then it may be more useful and feel more natural if, instead of thanking me, you reciprocated the goodwill through subtext.