Wanted to circle back. First, thanks for the advice! I followed daniellam's suggestion and checked my itinerary on checkmytrip.com -- lo and behold it was showing the old ticket number.

I called AA to get this sorted out. The first agent was super professional and tried to help but couldn't get hold of anyone at CX on a weekend. The agent today was difficult and flatly refused to contact CX. I eventually asked to speak to a supervisor who escalated to the Cathay liaison. For some reason it was not as straightforward as you would think - I was on hold for a good 15 minutes while they worked on it.

In the end the supervisor told me CX was unable to update their records with the correct ticket number (!) but would document the issue in the reservation notes so I won't have any problems flying. Checkmytrip.com still shows the incorrect ticket number but I no longer get the "Trip has not been ticketed" warning on the CX website.

Another one of those unexplained little mysteries of life I guess.