Don’t clean any more than you need to, so remove any substrate that’s peed on or otherwise really isn’t clean enough but always leave some of the old substrate, as much as you can really to retain her scent.
If you do the nest area always leave some of the nest.
Same goes for the food hoard, you can either leave some of it & add some fresh mix if it’s looking a bit old or just replace it with fresh mix.
Good point about the playpen, do you take her out when you clean, it’s always best to put them somewhere safe you can keep an eye on them when cleaning, some hams are fine with a bit of spot cleaning while in the cage but anything more than that you do need to take them out.
I wouldn’t worry too much, as long as you don’t overdo it they soon get over it.
Put lots of tissue in the cage afterwards so she can collect it up to add back into her nest.