[cypher]

That box will be fine for now, just cut the base out & make a hole on one side for a door.
It would be best to take him out while you rearrange things if you can, if you try to do it with him in the cage it will be stressful for him. If you have a carrier then you could put some substrate in that for him then try to get him to climb into something you can transport him in & put him in the carrier while you change things.
It will be stressful for him & will take him a little while to adjust but it would be more stressful trying to keep the tube clean & healthy tbh. Give him a few days to settle after you've changed things & don't do any more than spot clean pee & he should be fine.

I meant to say before that if you do upgrade to the hamster heaven it would be best to not use the tubes & penthouse, it comes with blockers for the holes, or you will have the same problem again.