I would hold off on the cleaning. Maybe you're doing it too often? Usually it's recommended not to clean anything at all for the first two weeks while they're settling in and not to move things round in the cage. Except possibly a little bit of spot cleaning the area they pee. They don't like people stealing their poops
They sometimes hoard them for extra food supplies (they eat them sometimes and have two stomachs so can redigest vitamins etc from them). An older tamer hamster might be ok with you doing some spot cleaning while they're in the cage but will still tend to anxiously follow your hand and check what you're doing!
How long have you had her? I would go back to square one. Leave her alone for 3 days, and don't clean anything for two weeks - doesn't matter if it gets a bit whiffy. If she's a dwarf hamster it's unlikely to stink of pee in that time as they pee so little. Then just spot clean the pee bits if you know where they are and they smell. If it's the sand bath, rather than change all the sand, just scoop out the wet bits and add a bit more sand and mix it in.
In other words take it very slowly and infrequently with the cleanouts. I wouldn't do a full clean out. The more substrate you have the less often it needs a substrate change especially if she uses a sand bath. You could go a couple of months without needing to change the substrate. And even then it's best not to clean everything else at the same time as it removes all their familiar scent. They scent mark the items in the cage and make scent trails to find their way around and feel lost if all their scent is removed. So if you do change the substrate, maybe add a bit of the clean/dry old substrate back and sprinkle it on top. Then do the wheel a different week and any toys etc a different week again.
Also when cleaning out, don't throw away the hoard or the nest. If they are pee'd in you'll need to remove most of it but try and leave some behind and then add new food in exactly the same place to replace the hoard. And add a pile of torn up strips of plain white toilet paper so she can rebuild her nest. If the nest is pee'd in try and leave a tiny bit of dry nest behind that isn't wet even if it's slightly whiffy and let her rebuild it with the new paper.
They are the most protective of their nest and hoards. Don't worry - I am sure this will settle down but it might be an idea to kind of start from scratch as if she has just moved into the cage and leave everything untouched for a couple of weeks. Give her a few days alone and then maybe get her out for some taming by letting her jump into something - a mug or hamster ball - just to lift her out of the cage/transport her somewhere. Either the bathtub (dry with plug in and a couple of toys - eg tubes or a mug on its side) or a large box. Mine have never liked a box! She can run around in the bathtub without hurting herself.
It could take a few sessions of bathtub time. They are much less territorial out of the cage but if she is anxious and biting it will take time for her to learn to trust you. So wear gloves while she's in the bathtub so you won't feel so anxious too.
You can start with just trying to stroke her on the back with one finger while she's running around. If she turns to bite then you have the gloves on. Leave it a bit then try again. Maybe 2 or 3 times the first session. Leave her another few days and repeat. She will start to get used to being stroked on the back by a finger and stop trying to bite it. You could use an old toothbrush at first so it's more at arm's length.
Once she accepts being stroked on the back gently by a finger then move on to putting your hand flat on the bottom of the bathtub, palm up, near her and let her run over it but don't try and pick her up or chase her round with the hand. Then try that with some sunflower or pumpkin seeds on the palm of your hand and see if she walks on to your hand to eat them. If she does that you could try without gloves the next time. But wash your hands first as if you smell of food she might think you're a tasty snack! Just use plain soap - anything floral or with honey in can also smell tasty!
It can be a bit slow or it can happen very quickly but once she is less scared and trusts you she will stop biting - hopefully! You could also do the tissue trick meanwhile. Put some sheets of toilet paper up your sleeve next to your skin, or down your bra, and leave them there for a couple of hours. Then tear it into strips and put a pile in the cage - she will take some for her nest and it'll help her get used to your scent.
But I think the main thing is - pull back on the cleanouts until she is tamer and more settled and even then not too often. Hamsters are quite clean little things really - they keep themselves clean. Their poops aren't dirty or smelly, they're like little hard seeds (and edible!) so unless they really start taking over in a big way I would just leave them. Their pee is the only smelly thing but spot cleaning can be difficult if you don't know where they pee. However if you have plenty of depth of substrate it should go some time and she pees in the sand bath you can just clean that out every 5 days or so or even just scoop the wet bits out.
She is probably getting more stressed and anxious about her cage and hoards, being taken out and cleaning etc done - so I'd just leave her to settle and not do anything in the cage for 2 weeks. Then after that, if it's just sorting the sand bath/potty do it when she's asleep and wear gloves just in case.
If she is associating being taken out with her cage being different when she goes back she will be reluctant to go out of the cage. So maybe when you do the first couple of taming sessions in the bathtub, resist the temptation to clean anything or do the sand bath. Then she will feel more confident that everything is the same after she's been out of the cage.
It's just time and patience and not cleaning out too much xxx Also when doing a clean out, best not to use any strong smelling cleaners or disinfectants as they have a very strong sense of smell and it can upset and stress them. There is no need to disinfect unless there has been illness or disease, so just warm water is fine, or warm water with bit of dish washing liquid in but then rinse well.
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