Went to Hoover Dam, got mission to deal with Great Khans. Went to Red Rock, quest arrow pointed toward Khan Longhouse. Went in, talked to Papa Khan. Killed everyone in the house. Nothing. The arrow still points to the house and i cant move on in the quest, even though i have killed the Papa Khan. I have been back to Colonel at Hoover Dam, she says get on with mission!?
I ran into the same problem. If you don't kill Papa Kahn without being detected (while he's sleeping or something else), then what you are missing is that you need to kill most if not all of the Kahn's in the entire area, not just in the house. You need to search the entire Red Rock area and kill at least 15 Kahns. You can read more on the Fallout Wikia about this quest.