I also hear vinger works well to get rid of the urine smell that the rabbit could smell. With my buns, if I left a box there for a little while, it would break the habit and then I could remove the box. You might need to leave the box there for a little while and hopefully it will break the habit and he will forget about it once you remove the box. Just make sure the smell is gone or he may start again.
Mom to Chase, LB, Ava, Charlie, Brenna and Ru!