Are there any noises or things that are spooking him potentially? Or do you think he’s just upset being penned up since he’s free roam?

Have you seen his posture when he does thumps? Usually if my bun is afraid he will be rigid, standing pretty stiff and up right. Typically I’ll look around to see what he’s looking at so I can help resolve if. It’s mostly a random laundry basket I brought in that was then deemed to be an intruder. on the other hand, if annoyed his body will be more relaxed but he’s just expressing his disdain for something — like being penned up. maybe he just wants the luxury of your chair in the lounge!

Rabbits can sense things that we cannot, so it is possible that he has been picking up on something that you cannot perceive– in which case, there’s not much you can do but let him habituate to it. Regarding the environment, just make sure there is a place he considers a “safe space” he can go to if he is feeling scared.

I saw a similar post elsewhere and I vaguely remember that it had to do with outside critters or a mouse go into the house for that person. Turns out their bunny was able to sense the mouse in the house faster than the hoomin could find any signs of it! hopefully this isn’t your situation but i though i would share it

Have you tried a night light? I know it sounds weird, but some bunnies like having a low light (like it’s dusk) and it makes them feel safer.