You can apply an SWU to a pax with a BAEC number. So no need for the AA number at all. AA/OW systems make it difficult to switch FF numbers- the first one entered is "sticky"- you think you hav changed it but it posts to the first account entered. If you do switch after clearing i will guess that won't help make it less "sticky" .

I would expect miles/credit for the fare paid but you might get a pleasant surprise.