Originally Posted by
Microwave
Unless something has changed recently, you definitely can upgrade a companion on another PNR. Just call your elite status line with both PNRs handy and request it.
Wow, I had totally forgotten that was possible, but it's clearly documented on aa.com and in the wiki:
AAdvantage elite status members can request an upgrade for a single companion traveling on the same flight using 500-mile upgrades as payment
If your companion is booked in a different reservation, call Reservations to link the reservations
Mea culpa!