I think Cipro not only kills the harmful bacteria, but helps the nem to expel the dead zoox, which is a good thing. I also think too much Cipro can cause a nem to bleach, but this is also okay because the zoox population can come back from literally nothing.
If the nem does not respond to Cipro or Septra within a day or two, then I think it will die. There's a very small window for treatment after the nem deflates. If it can't reinflate, it can't take in the Cipro. No med intake = dead nem.
If treatment is to work, like in humans, it needs to be administered for at least 5 days or the bacteria won't be completely eliminated. Again, IME, if the nem remains deflated by day 3, there is a very high likelihood that it won't make it.