As a Gold Member you can upgrade on board. The chief flight attendant can deduct the miles. Perhaps this option would work if there are seats and the check in agent can not process it for you.

If you are using a travel agent next time, just have them ticket it using EK's three digit code rather than AAs. You won't notice any difference on your end, AA will still get the revenue for your segments, and EK can do what they need to do to process upgrades.