TMI: Bacterial Vaginosis

So I had to go see my gyn today and I have Bacterial vaginosis. I've had it before and I've done everything to keep it from happening again. I've changed my soap, toilet paper, undies, laundry detergent, stayed away from sugar, lost 160 pounds in the past year. Everything! I even take a daily prebiotic for vaginas health. My gyno doesn't know why it keeps happening. Anyways, my concern is that I'll be in my fertile window starting tomorrow. Will this effect me as I am ttc? I'm taking prescription Flagyl and a prebiotic all natural suppository. I'd hate to have to wait another cycle. This blows. ?