Bv at 11w4d

So I went to the emergency OB department and they said I have bacterial vaginosis then informed me that this can cause miscarriage. They prescribed me Flagyl and told me this also can cause miscarriage. I of course freaked out and messaged my regular OBGYN and he told me not to take this medicine. He wanted to see me tomorrow to rerun the wet prep And prescribe me medication himself. however I am having extreme symptoms today such as pelvic discomfort and itching/burning at my vagina has anyone went ahead and taken the Flagyl and everything turned out OK?