Oh my, did the vet recommend any additional tests, explain why or about the necrosis in her throat? Has she finished with the medications given? I'm unfortunetly not familiar with this disorder and what the causes would be. There seems to be an immune system relationship from what I've read quickly after googling. Perhaps something to boost her immune system would be helpful.
It seems like the couple of days of eating again may have aggrevated the necrosis again? How is she doing today? I wish I knew more to suggest.
From what I have read, dogs tend to be more acidic and their digestive track is shorter than the humans.
Many thoughts of healing go out to you and your little friend. They are special, aren't they!