He obviously considers the other box the place to go. This may be a strange suggestion and may not work, but perhaps when you shut him in at night, take the litter box from his play area and put it inside his pen (still with the day’s poops in it).

Otherwise, I don’t think it’s particularly unusual for rabbits to do this. I had it happen with Bandit a couple of times when he was still half inside, half outside in his hutch. I would be concerned if he’s in his pen for long periods of time because obviously he may then be holding it for a long time which could cause issues. Your wife’s suggestion may be correct. 4 hours isn’t an abnormally long time for a rabbit to go without pooping if they’ve just been lounging around.

Is he perhaps using the box in his cage as a bed now?

My Bam did the same thing when my mother bunsat him. She has a 2 storey cage for him in her kitchen, and during daytime, it’s open so Bam can go and come as he pleases. But for safety’s sake (risk of hubby accidentally stepping on bun), she closed it during the night. Bam didn’t go in the box inside the cage but ran out first thing in the morning and went in his outside box. Like he held it because he didn’t want to go in his own “living-room”. He doesn’t have a cage here in his proper home, so he’s used to having lots of space and his litterboxes are several yards away from his favorite lounging-spots.

Pippi has a strong preference for going outside, and dashes for a corner of the run when he goes out in the morning, and the tail goes up and stays up for quite a while. When we get a rainy morning, he sits by the back door, and starts thumping, as he wants to go outside to do what he doesn’t want to do inside.

He used to thump around 4am, and when I went down to see what was wrong, he’d hop towards the back door, as if to say, I need out. Needless to say he never got out at 4am, and eventually stopped the 4am thumps.

I guess when they’ve got options, they opt to go further away from their “burrow”. Just like wild rabbits won’t toilet in the burrow.

It’s funny, when I just had Jersey and Rumball, I would let the roam around outside in the garden. I left the back door open and was always amused when they’d hop in, use their litterbox then hop back outdoors. They never designated a spot outside to use. A few years later they detected any other rabbits had been out there, they toileted everywhere. By other rabbits, I mean more I adopted or had looked after.