Re: Deleted Scenes .fgd
my guess is that's for performance reasons. the environmental effects aren't cheap, and this is an 8+ yr old game engine (quake) on the inside.
trigger_incognito -> the beginning of the turncrank mission has you going in under-cover (incognito). I'm pretty sure the trigger is used to toggle this state on and off. It prevents the enemy AI from treating you like a target while 'under-cover'.