First of all, what Triple A does means nothing. There are many, many Triple A errors with regard to the rule book.
One of these errors is that Triple A give you a retreat option when there are only transports left, but this is illegal because you can’t retreat from units that have no attack value (transports and AA guns).
However, you had defending aircraft still in the zone. See page 20 of 2nd edition Europe rulebook.
Condition A: “Once all units that can either fire or retreat on one or both sides have been destroyed, the combat ends”
You have subs that can fire. He has planes that can fire. It doesn’t seem to matter that they can’t possibly hit each other. Combat has not ended. It appears that you can retreat the subs because both sides still have units that can fire. You could even wait until you have sunk all the transports, and then retreat from the aircraft.
I am not 100% sure on this answer because I can’t find anything definitive in the rulebook that answers this question. You need to ask Krieghund to be 100% sure.