If it makes Jean feel any better, Peter totally left Unity relatively quickly when he realized it was reckless (who invites Deadpool onto a team?) But yea, the AvX was a trying time. He's definitely met Jean before, plenty of times, but not this time-displaced Jean that I know of, but also possibly? I never doubt Spidey's met someone in the comics!verse.
I love Bobby! And Peter loves Bobby! Friends.
Hi Doc! You helped the world forget Peter and Spider-Man were the same person. Go you!