If you switch at check-in or at the gate, be sure that the boarding pass you use has the FF number you want credited printed on it. If it doesn't, ask them to reprint it so it does. If you have a boarding pass which shows that you wanted Asia Miles and for some reason they don't credit (highly unlikely once it shows on the printed boarding pass), you would then have an easy retro-credit situation.

If the boarding pass shows your AA number, it is your word vs. the printed word. You know which wins.