Good question, and that's what the check valves are for. unless your baffles are extremely under-sized/restrictive it should work out fine because all exhaust collectors have a "pulse" and it has a lot to do with lobe separation (the time in degrees that the intake and exhaust valves are open at the same time) the exhaust does not flow in one direction only.

Easy to prove, start your car/truck and get a piece of paper and hold it at the exhaust tip, it will pop back and forth, if you have a bad exhaust valve it will pull in harder than push out, sometimes even tearing the paper in half. Kind of cool if you think about it.
