My general experience is that if Reservations approved it, that the check-in agents just collect whatever it says to collect.
I rarely see or hear of check-in agents browsing through the fare rules to see what's what unless they are looking for re-routing, change fee, and other stuff.
That said, if it's SOP not to upgrade companions in a particular market (like London), those agents there might be more aware of things.
I'd just go ahead with it, and if a check-in agent tries to deny your companion's upgrade, I'd just stick to my guns (and play dumb) and say "Well United approved it. And they gladly took their upgrade coming here. Plus how am I supposed to know they shouldn't have."
If that doesn't work, as to speak to a supervisor or Station Manager.
Good Luck!