Arabic definitely took over language-wise, but ethnically speaking, I know at least the Copts and the Nubians stayed put. There must have been some Arab migration into Egypt, but it's unclear how much.

It's true that ancient Egypt had its ups and downs, but I think perhaps what helped them recover is that the downs were never so long that they forgot what they were capable of, culturally speaking. I do think agricultural power lessened in importance over time, but I don't know if that was the cause or what necessarily took its place. Perhaps it was trade and/or naval power.