If I'm altering a mission for whatever reason, AFTER the main sim has loaded and I want to modify the mission I exit the mission but keep the sim open and shrink to desktop.
I then open the mission file from the desktop, after altering it I can quickly open the sim from the task-bar again to load the modified mission.
Having said all that it is annoying when you are modding to keep waiting for it to load every time, I know on some occasions you need to exit the sim altogether for it to load for you to test your mod, then back out again if it needs more tweaking.