There are fares with no co-pay, but they're high enough that you'd notice -- you wouldn't be adding extra stops to try to get them. There are no cases where a $600 co-pay is supposed to be waived. I agree; it sounds like the system got confused and gave you a massive discount. Did your upgrade clear, or is it still waitlisted?

If it were me, I would expect to be asked for the $1200 at any point until the day of travel. If you take that approach, the only possible surprise is a positive one. :-)