We've done something similar - used AS miles to upgrade and then credited to AA. If done at check-in it works just fine. In fact, one time we changed it over the phone a few weeks after applying the upgrade. At the time of the upgrade we were told that we needed to keep our AS numbers in there. So we did...for a while.
Cheers.
AS mileage upgrades require crediting to AS? Pretty sure that isn't the case on AA since one doesn't even need status for a miles (+ copay) upgrade.