This thread ist old but... the issue/bug is still there...
We tried to create a High Commander vs Team (coop) mission but it doesn't really make fun because once discovered, players marker won't disappear from the H.C. map.
The issue has already been submitted 10 months ago but not fixed yet:
http://dev-heaven.net/issues/2073
Try it yourself in a SP test mission:
BLUEFOR player as High Commander (+ some AI) at the blue side.
OPFOR armored vehicle (e.g BMP) with 0% ammo, near player.
Let the vehicle drive far away (waypoint).
Start the mission, enter the H.C. mode (CTRL + SPACE) and watch the map:
the red marker doesn't disappear even when the vehicle is 3 km away.
Is there a work-around maybe?