Glitch? Maybe?

So earlier this week as I was playing. I was on the last mission of chapter 2. But I was holding off for a bit, just doing exploring and all that. To the point. The Rhodes Gunsmith. The man he has trapped in the basement. I had the encounter when he was calling out, but it never updated to the log. So I figured I had to wait for something. It wasn't till a little later, I broke a man out of a prison wagon, who gave the tip, and it went to the log. So I went back. Couldn't do anything about it. Waited longer. Finished chapter 2. Hadn't done any chapter 3 missions. I went back, and there is an x where he should be. So apparently he is dead, and there is a question mark in between the two buildings. I've since done the first mission for chapter 3, nothing has changed. Is that encounter just screwed?