It sounds like she is still unsettled and moving things and changing things has probably delayed her settling in again. Some hamsters hate anything moving even an inch - our last Syrian was always like that and got completely freaked if anything moved to a different place or was taken out. He didn't mind a new thing being added in and found that quite interesting - as long as nothing else had moved! They all have different personalities and when you hear about people moving things and changing things to make it more interesting I think that depends on a lot of things - a) how old the hamster is b) their personality c) what's been going on in their lives and d) how you do it.
So if she had been in the cage for a year with everything the same then adding or replacing something might be accepted better. Taking the Penthouse out has probably wound her up but it's better removed as it's a pain and the tubes get blocked up. Also those little houses on the shelves are too small. Our last hamster decided to nest in one and it kept getting smelly and the top kept popping off as he stuffed too much stuff in it.
It sounds like it's a stage of getting the Hamster Heaven right and giving her time to adjust to the changes - she probably feels like she's been invaded, robbed and being chased by a broom!
If there isn't a house they think suitable for nesting they will nest under a shelf sometimes - but they like to do things their own way.
So as humans we have to curb the urge to keep tweaking things too much. She may or may not accept the bendy bridge over her nest or you may find it tipped over and moved! They are actually very tidy and like to rearrange things in the cage themselves sometimes and will moved substrate all over the place.
Now the Penthouse and little house on the shelf is out it sounds like it's nearly thee. The hamster heaven is a lovely cage but works best without all the plastic stuff it comes wiht. It helps to have one shelf but there isnt room for both as well as a syrian sized wheel.
The one thing they get very stressed and fussy about is their nest and hoard (two things!). So if the nest and hoard got thrown away when you took the house out she probably will go bananas and not feel safe. Hence trying to chew her way out.
Getting her to settle down is the tricky bit - it will happen in time but there is no set formula. I'd say a combination of letting her out regularly and leaving her alone. When our hamster got like this after being moved to another house and coming back it took two weeks for him to stop bar chewing and going bananas. He wanted to be in and out every five minutes. In the end I set up a playpen round his cage (which was on the floor) and just left the door open (same door as your cage) and just let him run in and out and have more space but he was still hyper. We then tried turning the lights out and going to bed early (he only seemed to bar chew when we were there). That slowed things up a bit. But what did it in the end was a full cage clean (different circumstances maybe) as he could still smell the other house on his cage I think (and maybe other hamsters too). Normally that would stress them but it sort of shocked him out of it and he calmed down andwas interested in the new chews.
So I'd suggest leaving everything alone for now - even if it's not ideal - for a week or two. Meanwhile let her out as much as you can and don't change anything while she's out of the cage (they come back and freak that someone has messed with the cage when they were out!). Weave some cardboard round the bars to deter the chewing and maybe hide the odd treat in different parts of the cage. And you could try playing soft music.
It makes us stressed too when they are like this but just keep at those things for a couple of weeks and don't clean anything - even spot cleaning - unless it gets excessively wet and stinky in the pee area. So she feels a bit more like it's her territory.
After the two weeks I would get the cage just right and then leave it like that for a long time. Does she have a wheel that's big enough? Sorry if you said before - can't remember. That is another thing that can make them bar chew for attention or get hyper if they're not using the wheel because it's too small and uncomfortable.
With the hamster heaven I would have the wheel at one end at the back of the cage and the solid shelf at the opposite end - and add a house that is dark inside - a shoebox or tissue box would do but if it's open underneath and sat on the substrate it's better because then she can have normal behaviours - like burrowing down to keep warm and burying hoards under her nest. A shoebox may be too big to fit in there with the shelf and wheel. I found I couldn't fit a house under the shelf easily and in the end I started with an empty cage and no shelves and added a guine pig house with a flat roof - which gave a large dark area for nesting and also doubled up as a shelf. Plus rat sputniks are good in the hamster heaven - they hang low from the roof andmake something to sit under and climb into.
I wouldn't use any of the plastic tubes that came with the Hamster Heaven - just the solid shelf.
So in a couple of weeks just spot clean a little bit - any pee - change anything that needs changing and add a house. If you put the bendy bridge over the house entrance it will tempt her inside because it'll be nice and dark inside and if it has a flat roof then the bendy bridge then makes a ramp on to the house roof.
Then when she goes back I think she'll settle. Leave her nest and hoard where they are - she'll take anything she wants to the house. She might change her pee place then so you might need to move the litter tray when you find the new pee place.
Basically it's been a lot of change and she's freaked out. They also do need somewhere dark to retreat to to feel safe.
I'll add a couple of photos of my old cage set up (which was a bit too fulll and cluttered!) It's exactly the same cage as the hamster heaven but smaller bar spacing (Savic Mickey 2XL) and didn't come with all the plastic bits and pieces. I actually bought the hamster heaven shelf to put in it initially but couldn't get on with it - it wasn't flat and could never get the height quite right. So iwas quite glad when the ladder snapped and I took it out and put a flat roofed house in instead. And boy that caused major issues when I changed that! Our current syrian is more laid back but some just hate any change at all. They also like things to be just right - ie easily accessible - so get fussy if there are things like that (I put the sputnik too close to the bars once and he was not happy with having to squeeze into it!).
So when setting up - it's access first - really start with it simple - house, wheel, shelf, and then add a few floor toys or hanging things. But not those hanging barred ladders - they're a bit dangerous.
Our poor last syrian had so many changes to get his cage right - so now i just keep it simple with toys.
This is when I first had the cage set up. It didn't work. The little house n the shelf was a problem, and the hanging ladder was dangerous so had to come out. The little wood house at the front he ignored because I think he decided it wasn't big enough and wasn't dark inside.
Attachment 46509
So I changed it to this which worked much better.
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But he didn't seem that interested in using the rat sputnik so I added a tunnel tied to the roof leading between the house roof and the sputnik and he really liked that roof run. Then adding bedding to the sputnik made it one of his favourite places. Looks a bit heath robinson though.
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He was so big and heavy his wheels kept breaking so I ended up with a 12" wobust wheel which was a bit too big for the cage (hence he got upgraded to another cage eventually).
This was the final set up. Changed the guinea pig house for an even larger house with a lift off roof. He was very happy in this set up with his litter tray inside the house - but with the large house and huge wheel he definitely needed more space by then. You don't need such a large house and wheel though!
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With the lovely big front door on the cage the sputnik was low enough that he would climb in and out of it when getting out of the cage.
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It became his favourite place - after his house