Would it be supercilious to thank someone for updating?

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.