Yeah, that's right, you just have to call them and explain. Here in de US they are always very helpfull and credit the miles whithin 3 hours our so.
About the point that Medico is making: he is very right. Had to book a flight to Europe yesterday and the American-'Swiss'-lady said that Gold members do not have to wait for Z-class (Y upgraded) seats.
If you show up for checkin AND there are C-seats availabl you can upgrade no matter what. And.... nowadays loooottts of C-seats are avaiable.