You could try putting his cage litterbox there instead, when he’s out.
Other then shape, how do the 2 boxes vary? If he has aversion to this box you could try completely new one, or place puppy pee pads or towels down in its place to test the theory. If he consistently uses that, it could tell you the issue likely is the box for some reason.
I was wondering if maybe something had scared him while he was in the litter box and now he is afraid of it,
That’s possible. Perhaps you could experiment by placing a cardboard hidey box with 2 entry points over top of litter box?
I read on HRS years ago that rabbits toileting right next to the litterbox is like underlining a signature. Making an emphasis on “this is mine” I suppose.
It’s the thing in the space that is specifically his. Do you have other pets? Have you had other animals or people visit? I even read an account of a tradesman coming to the home that was enough to cause a rabbit to become territorial.