I have used AC SWU's to upgrade and credited the miles to my M&M account and always got the COS. The way to do it is, check in, hand over your cert, then just before you are to board have them change the FF number. It can also be done in the lounge, but some agents refuse to do it (if so show them the line where it says you only have to be E/SE it does not say miles have to be credited to AP)