A similar situation happened to me from Perth to Sydney. I did an upgrade from Economy to Business, which was done over 2 weeks prior to departure. They did not have enough Business Class meals for the number of people in Business Class and the flight service manager pulled me aside to say as i was the only person in the cabin who had upgraded i would not receive a meal. As someone who regularly pays for Business Class, i did not mind this so much, but I did complain when I got back to Sydney and they gave me a $100 credit as a gesture of goodwill.