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To be totally honest I don't think that tube looks like a healthy place to sleep at all, even more so if you get food & pee in there.
It will upset him if you remove it but long term you'll be doing him a favour, he probably won't use any other part of the cage or another house so long as you leave the tube there but he will adapt if you remove it. It can take them anything up to a couple of weeks sometimes, often a lot less, to really get used to a new set up but given a little time & just left to get on with it they do sort it out for themselves.

ETA Cross post there I think!