His scenario is different than yours. What happened was that his upgrade cleared after he has checked in for the flight in Y; he noticed it while he was in the MLL so the agent simply offloaded him from his Y seat and rechecked him in for J.

You won't have any issues in your case, both certs (for yourself and your friend) will be lifted in YYZ. He can check in like usual and because he is in Y for YUL-YYZ, the prompt asking for the agent to lift the UG cert will be on the YYZ-POP flight. You can't do his upgrade online because he's not on the same file as you (given different originating file), you'll have to call in.