Surviving an encounter doesn't clear the hex, although I can see why that might be assumed.
Hexes are "clear" before they are visited, "marked" when they have been visited, and "cleared" when you are resting at base (one per turn), erasing the "mark" and making them "clear". Trooper should only have encounters on "clear" hexes, not "marked" ones. Hope that clarifies!
Definitely agree there is room for further development. Glad you're enjoying it!