[Corsair]

When you start your patrol, you make a save far enough from harbour (100 km to be safe).
You run SH3 Gen once on that save (basically SH3 Gen writes inside the save and makes a backup). The infos on the map are carried from one save to the other, so you don't need it anymore till next patrol start.

PS it depends if you use the mission feature (I do) this is why I only use it once otherwise you get a new mission everytime. If you don't use the mission and want updated info, then may be you can run it several times as BBW said above.