Hi.
Yeah, I had the same problem. And was in a similar situation to the guy in the other thread who was a stealth build.
There are a few relevant checkpoints.
1. Before the Darcy fight
2. Just after killing Darcy (Checkpoint 3 comes almost as soon as you leave the area, so make sure you save as soon as possible)
3. Just before you turn the corner after leaving the Darcy area
In my experience, checkpoint 3 never worked, but checkpoint 2 sometimes works.
Also, with Checkpoint 2, sometimes the helicopter would not be there but the gate would be down anyway.
I eventually finished the area by reloading Checkpoint 2, the helicopter wasn't there, but I finished the area by killing the first few enemies before going around the corner with the truck, then going Shadow operative and running around using takedowns on all the enemies. The gate was down even with the helicopter's absence.
Other times the helicopter wasn't there but the gate was still up.
So, my recommendation is to get past the fight with Darcy, save the checkpoint (Checkpoint 2, above) and keep reloading that one until the gate is down, helicopter or no.
Annoying, but at least you don't have to fight Darcy again, which took me about 12 attempts.
Good Luck,
Caveman42