If he has been ill, then it may take some time for him to get back on track again, but this seems to be an ongoing problem, right? I would probably take him to the doctor if you feel he has lost weight. If it makes you feel any better, Riley has been doing the same thing with his food lately. I had started him on vitamins with iron, but these seemed to upset his tummy and made things worse. And with his teeth again, he is just totally off.
Is it the milk in his cup that he doesn't want? Would he take it in the bottle? But I know you have been working hard to transition him to a cup.
Sorry I have no real help to offer, but will lurk here if that's okay, to see if anyone has any ideas.