This seems like a tough position to play in. If the BB is the type of player who would check the nut flush draw on the flop, I think you have to consider folding. I would really worry about ATs or similar hands. The odds were certainly right to check/call the flop with a flush draw.

I think also you have to be concerned about a hand like TT. I wouldn't put it past some players to slow play trips with several people in the flop and a flush draw on the board.