Just an FYI, if you are also supplementing with Fish Oil and there is already an adequate amount in the food you are feeding you can actually cause more harm than good. I had a dog whose wound was very delayed in healing and it finally closed with a different treatment and taking him off of Fish Oil,I had been feeding it as I always did even though I had changed foods, as it can block the infammatory response needed for wound healing. I feed Orijen and there is no need for additional Fish Oil supplementation on it, I would suspect that the TOTW is the same.

I would see if the vet can scope her ears while she's sedated and actually see what is in there. It could be that scar tissue is built up and trapping debris in the ear.
A follow up culture of the bacteria to pinpoint an antibiotic if this doesn't respond to the Keflex. Has the vet suggested a Chlorhexadine bath for the skin or Nolvasan for the ears?
Hope your girl has some relief soon.