the black doesnt sound to me to be ammonia burn, sounds more like healing possibly from the meds and infection.... is there any chance you can post pics?
I just took this picture. The medication treatment for Velvet ended last Sunday, and these black marks started on Weds. The marks started NEAR the edges of his fins, then filled in to the edges of the fins. They seem to be a little lighter today than yesterday.
BTW, he is a new fish, who I bought with another comet who died from Velvet because I didn't know what it was at first and started treating too late. They were quarantined in separate tanks just because they were new fish. This one didn't show signs of sickness until I had him for 2.5 weeks, and I treated him with Maracide and Maracyn, which worked wonders.