I've went from my forge with blue+1 back to my stock bpv, and the car ran horrible, 2nd gear would hesitate every 3rd or 4th time going through the gears. I reflashed my map, and it went away. I got my forge fixed, and back on with yellow+1, and did not notice a change from stock. So if you notice a drastic change in the way the car drives, I would say reflash your map, and see if that takes care of it. Also during that time I tried resetting the ecu, and it did not help at all.
I think Cobb recommends use of the stock BPV for all their tunes. With a custom tune by a third party tuner, that may not be the case. Ask Travis at Cobb.