To re-arm and refuel, press Ctrl-R while playing.

If your aircraft is heavily damaged and your sure it's not going to make it, don't worry about it. Just exit the game NOT THE MISSION. Then just go back into the game. When you exited it saved your pilot. You won't get the points for the mission you were on, but it's better than having a dead character.

Unverified. To be invisible to your enemies you first need to select the 'Free Flight' mission. Once able to fly, crash into the first building you see (it doesn't matter which). As soon as you crash, end the mission.

The 'Free Flight' mission is a simulation, so you don't die. The game will register your chopper as dead in the next mission you attempt, and enemies will not fire on you. You'll need to do this every time you attempt a new mission.