Hi

Are you sure he has really been neutered? Because they might have said he was fixed but it could have been false. So the best thing is to have a hay/litterbox combo like this  https://www.etsy.com/transaction/1351831534

This will teach him to eat and poop in the same area (as buns naturally do this) and I would put this and soft flooring in a xpen until he always poops and pees in there. Then you can slowly increase the amount of space he has. 

 Is there another bunny that you have and he smells him? It could just be that he is to old that he has never been taught to use a littler box and it might take extra time to break his bad habits. Even my buns that are potty trained, still leave some poops just because they don’t always make it to the litter box but they are still very well trained.

My neutered 4 year old is giving me tons of trouble as well, so I definitely feel your pain. T__T

I have some questions:
Is he pooping in his litter box at all? If not, he indeed is not “litter trained”. Does he have areas he will always pee/poop? Have you tried moving the litter boxes to that area? If there are multiple of those areas, have you tried putting a box on all those areas (not the spots he peed or pooped once, but the ones he will always go to)? You may be placing the litter box on an area he doesn’t like to pee/poop. Rabbits are clean but they like to choose their favorite spots to pee/poop themselves, if you decide another spot is better for him to pee/poop and place a box there rather than his chosen spot, he is going to ignore it.

Is there hay in his litter box? If not, put down some hay there. Bunnies like pooping while eating.

Do you have a fleece undergound in the pen? Some bunnies like peeing on soft things. Mine are litter trained but will always pee on the towels I lay in the pen. Try replacing the fleece with something that is not soft, such as vinyl.

If he is pooping and peeing in his litter box and he does it quite a lot, he is actually litter trained and the pees/poops are to mark his territory. In that case, do you have any other bunnies in your house? He may smell them and feel the need to mark what’s his for them. How often do you clean his pen? If you clean every day with vinegar or another substance that gets rid of smells, his smells keep disappearing and he will want to bring the smells back. Don’t thorougly clean his whole pen too often with vinegar or another smell eliminating substance, just spot clean when necesary. That way he will not feel the need to bring his smells back as much, as they’re already there. I thorougly clean the pen of my buns once a week personally and clean the pee/poopy parts with vinegar every other day (the pee/poopy parts are in the litterbox).