Wow, I feel really sorry for your snake.
If a vet prescribed antibiotic shots, I would give them to her until the rot goes away. This is a war here, don't let up.
Heres a segment taken from this snake care page:
http://www.redtailboas.com/instant/instant.html
Belly Rot/Scale Rot
"Clean the entire affected area by swabbing with a 50/50 hydrogen peroxide/water solution.
Must be thorough to treat the entire area because the damaged tissue could be in multiple places.
Apply Polysporin or Neosporin to the affected areas twice a day and work it in and under the scales.
Immediately clean the enclosure thoroughly. Raise ambient temperature to 88-90 degrees.
Consult your veterinarian as soon as possible, antibiotic injections may be required.
Scale Rot (Neocrotic Dermatitis) appears as enlarged, discolored (rust or reddish-brown), fluid filled scales.
Possible ulceration and breakdown of the skin and underlying tissue. Generally appears on the ventral scales (belly), and can be in one long continuous area or in separate spots. This is a bacterial infection that can be caused by damp substrate, inadequate temperatures, and dirty enclosures. Bad cases will also have blisters, and will require draining by your vet. Serious cases are life-threatening.
You must keep your boa warm and dry during the recovery process. If your boa tends to soak in the water bowl, it may be necessary to remove the larger bowl and replace it with a very small dish that would not allow soaking but still provide drinking water."
I really hope this helps, good luck caring for your snake.
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