WTH - I can understand your worry - I think I will be worrying about everything when i eventually get to start my PGD cycle. However, don't panic! Similar thing happened to me in my last cycle. Got more bleeding etc halfway into FSH jabbing. I didn't have any BT done at that time but few days later when i went for scan and BT - all was on track and I ended up pg with twins. I know the pregnancy itself didn't go well at all but didn't have anything to do with the weird AF.
I hope BT result is good - I am sure you will be fine!