I'm sure with a vet appt and good antibiotics she will be just fine. Scales rot occurs from bacteria getting trapped under the scales. And it infecting the tissue and
The scales creating blisters
And infection. Chewing mites could definately help that along. Even though the mites may be gone,the damage had already started. Scale rot is very treatable when treated with proper meds and husbandry. Until this starts getting better id switch her to paper towel sub. And have betadyne on hand if you don't already. Combined with the antibiotics I'd wipe down her belly and any other infected areas with the betadyne once a day or do a soak with a betadyne/water solution once a day. Either or will work. Also just to further prevent anymore possible Bacteria I'd change the papertowel 1x daily. I hope this is helpful.
Morgan