The involvement of AA is unfortunate, and probably will turn out to be the source of the problem. It will be interesting to see what CX does. I've had several experiences with AA canceling flights by mistake -- in my case they could be reinstated so no damage was done. AA has a very aggressive program to cancel onward reservations whenever they "think" that you have missed a flight; they've canceled on a flight time change -- clearly a flaw in the system, as I flew the flight. Maybe something like that happened to you (a reservation not canceled properly so it showed that you failed to fly). In which case all CX knew is that you had canceled your reservation. You would have had a hint that your reservation had been cancelled as CX confirms all F reservations out of the US by phoning the passenger within 24 hours of the departure time to reconfirm; but of course the onus should be on the airline and not you. I try to avoid these problems by confirming with the flying airline whenever the reservations are through another airline (and about 5% of the time this avoids a problem -- so this is a surprisingly common circumstance).
My guess is that CX will offer a free upgrade on a future flight as compensation. Personally I would have taken the offer of F on YVR-HKG.