"... instead of addressing the crowd about it, he deals with it in a transparent* way keeps the show going like nothing happened. Amazing, and classy!"
"it" = the audience is clapping on the 1 and 3.
I think there's a lesson here that goes beyond music. I'm thinking of analogies in social, political, and business relationships. You're performing within a group that is getting it wrong, and you could stop and point it out and try to show them how to behave better, but instead you do something that they don't even notice that makes them start doing it right. Of course, if you had this power — Connick power — you could use it for evil.
Maybe Donald Trump has Connick power!
* This use of the word "transparent" may be confusing. We tend to say "transparent" when we mean that a person is making his intentions and motivations perfectly clear. That's exactly what Connick is not doing. But "transparent" makes sense if what you mean is that the technique used was invisible to the audience and they continued to experience the music as if nothing had happened.
ADDED: Here's an ordinary human dealing with the same situation, sans Connick power: