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Unfortunately it really isn't good for them to sleep in the penthouse, the best thing to do with the hamster heaven is to remove the penthouse & tubes blocking the holes with the stoppers that come with the cage.
Apart from being disturbed easily it will get very unhealthy for her sleeping in there.
If you provide a nice large house with no base on a deep layer of substrate (fill the base part of the cage) & give her a nice pile of shredded plain white toilet tissue to make a nest too she should settle down again quickly enough.
If you don't have a large house you can use a cardboard box, shoe boxes are good, just use it upside down & cut a hole for a door.