His FAA CPL/IR is a standalone CPL, not one issued on the basis of a foreign (JAA) certificate. So that whole discussion is irrelevant.
And since he's got an FAA CPL/IR and even an FAA instrument instructor rating, I would guess that his medical exam would have been to keep his FAA CPL/IIR valid, not his JAA PPL. After all, if you own a very capable N-reg, which of the two would be more relevant?
If that was indeed the case, then the flight would have been completely legal. But as me and others have pointed out, the legality of the flight does not have a lot to do with what actually happened.