Those penthouses are a pain. Most hams seem to love them but they're so awkward and poorly ventilated. But you should take all of that bedding and hoard that's currently up there, or as much as reasonably possible, and use it for her new nest. So it won't be gone, it'll just have moved.
If you don't mind taking a few extra days you could take the penthouse away now and get her settled in a better nest while she's still in her old familiar cage then swap that nest over as it is. But it's a judgement call whether the smaller stress from that, plus then the stress of a cage move relatively close behind it would be better or worse than just switching the whole thing at once.
I would personally just do the whole thing at once so they spend less time overall having things moved about but you know your ham and if you think she would do better with it coming gradually then you do have that option. Either way, her nest should transfer as undisturbed as possible.
Note: Excellent username, my little syrian girl is also called Jin, as seen in my profile pic
