In the very first mission where you have to interrogate the lieutenant, I accidentally alerted some of the enemies/lieutenant and decided to use the quit to menu option in the hopes that it would restart the mission so I could go through stealthily. After I got back to the mission area, the lieutenant was nowhere to be seen. All there was was the indicator showing where he should have been. As far as I could tell, all the other enemies were all where they should have been. This is on Xbox One.