What was the clause?

It was something like that the app must have been "originally written" in certain approved programming languages. It basically targeted cross-compilation, but it was written so vaguely that on paper it appeared to even disallow native iOS apps if they began as a port from some other language.

There was briefly a kerfuffle about it, because various people were using other non-flash cross-compilation tools (xamarin? etc), and they worried their apps would get removed as well. But IIRC apple never actually enforced the clause, other than to remove existing flash-based apps and reject new ones.

But it did cause vendors of cross-compilers to lay of dozens of staff as the clause killed their business (Source: I work with someone who was laid off because of the clause)

I don’t recall Apple unpublishing my AIR apps. One of mine was among the first secretly submitted before Adobe revealed the feature publicly. However, I definitely remember after Apple added the new clause, when I needed to submit updates, those were stuck in approval limbo for many, many months. Then, suddenly, they all got approved in a flurry and there was never an issue again.

Adobe AIR is actually still available today (now maintained by Harman through an agreement with Adobe), and it can still compile native iOS apps that can be submitted to the App Store. This feature was never removed, and is still maintained to be compatible with new iPhones.