Hi,
It may just be me but that looks like a burn more than scale rot.
I think you need to take her to a vet to find out for sure though.
How are you heating the enclosure in terms of both heating devices and controllers like dimmer switches or thermostats?
Can you check the temps at the warmest part to make sure they haven't gotten too high?
Using a 5% bleach solution and rinsing it out afterwards shouldn't have any negative effects either.
dr del