The original ticket was in coach, but I was upgraded on the AS flight PHX-SFO before check-in opened. For the re-booking I got a boarding pass in eco from the check-in counter, then received a boarding pass for F at the gate before boarding. The confirmation email I received about the re-booking states the class of the new flight is Class: U(First).
Did you purchase the original PNR from AS, AA or elsewhere? For the purposes of crediting to AA or AS, U class, a complimentary upgrade on AS based on AS/AA status, is irrelevant. It will post on the underlying fare class purchased. You don't need to be concerned with that.
AS said they had already forwarded the flight details to AA, so they have fulfilled their duty. Essentially, it is out of their hands.
At this juncture, I would contact AAdvantage and determine the status of the flight in question, get it posted to AA and then ask for a reversal. Once you can show the flight posted and then reversed from your AA activity, provide that information to AS. If the original PNR was AS plated, I would also request ORC for the SAN-PHX-SFO itinerary.
James