Confirm in "The Boss Goes to Washington" caused helicopters to not appear and Pierce fell out of the sky with no copter available. Without the mod it was fine. There were other things in other story missions, characters talking but not being present, I didn't try to confirm but suspect were also caused by it. Just this one case broke the mission.
I'm running into a similar problem except Pierce gets the helicopter lands it I get in and then it is completely stuck and will not move at all of the ground. I can still shoot the guns and missiles and my character says he gets in the helicopter where is pierce with the helicopter. Sadly I don't see on here or on Steam's forums that anyone else is having this problem your is the closest to mines i've seen.