Booked a Q fare on LAX MUC in September and applied PP upgrade which went into waitlist even though the flight was wide open for sale in P till a day before departure. Checked in to economy at T-30 and got an error. Tried at T-29h and got a boarding pass in Y. Sometime at night (about T-15h) the upgrade cleared but the eco segment was not deleted. So online checkin could not resolve the dilemma. At the airport the agent was also confused and called his supervisor. He checked me out and in again which resolved the problem. Alls well that ends well.