I have experience doing this - some even without planning for it.
On my last trip with several OW airlines my Swiss Number was in the itinary. No problem changing it to the AA number at check in - had to do it basically every time when checking in.

Also the swiss number likley triggered the extra security check - on this trip i allways ended up with the special code on the boarding pass for the extra check. Seems that swiss program members are more likely to be terrorist than aa program members......