[cypher]

This is a very common problem due to the inappropriate design of the cage unfortunately & the cage is best used without the tubes or penthouse, just block the holes off.

She will be stressed initially when you remove the penthouse & tubes but you just need to give her time to settle down again, putting some of the old nest material in a new house will help her settle, try not to worry if she seems unhappy about it just wait for her to settle, if you remove it then put it back again it will result in the same problem & more stress.
Give her a nice big house (a cardboard box like a shoe box or something is ok if you don't have a good size house) with no base laid on a good deep layer of substrate so she can burrow down & make a proper nest & she should be fine soon enough.
The sooner you do it the better really & doing it while she's out of the cage is the best way.