Did you pre-confirm your upgrade? If so, what instrument did you tell UA you would be using? If a e-CR1 or e-SWU then just ring MP and ask for that to be corrected. If you upgraded at check-in then I can understand why 500 milers were automatically deducted, although you should have the option of providing any one of the three (or more) upgrade instruments. But I can think of no reason why you shouldn't ring MP now to say that you'd like one e-CR1 deducted and the 6 - 500 milers re-deposited.