I had the same issue. I upgraded from Biz to F using Asia Miles, but left my AA number in the reservation.

The outbound flight credited automatically without intervention.

The inbound flight did not credit and I submitted the Missing Mileage Request. That request got denied due to ineligible fare class. All I did was call the ExecPlat desk and ask for AAdvantage Customer Service, who had record of the denied claim. I explained I paid for Biz, upgraded to F, and provided them with my original ticket number (both ticker numbers were on CX stock). Call took about 5 minutes and miles (and EQM/EQP) posted to the account the next day.