Do you have enough litter boxes for your cats?
by rule of thumb you should have 1 box for every cat, PLUS 1 more.

Are there at least two boxes that are the large one he likes?
some cats prefer to pee and poop in DIFFERENT boxes. if there is only 1 his size and he has peed in it, he may refuse to use it.

so far this is all I can think of, I will keep my thinking cap on for you.