I've been on Flagyl for months. It's the only thing that works for me. Humira, 6mp etc haven't worked but Flagyl makes me feel a hundred times better. I'm not quite in remission but my quality of life is so much better on it.
The taste of Flagyl is brutal. I ususally swallow mine in a spoon of applesauce to keep it from touching my tongue. It helps. I think the general course of Flagyl is only about two weeks but I can't imagine it would fully close your fistula in that time. It hasn't helped my fistula in all the months I've been taking it but it sure does help the pain and bleeding.
Best of luck to you.