I also had this issue and made my own post about it. Didn't realize there was one open already. We're not the only ones with the issue as I found a reddit post from a few days ago of others with the same problem. They think that the hunter is supposed to despawn when you enter a safe area but the hunter instead just has his ai turn off and freezes in place and the game no longer considers it an enemy so it can't be killed or damaged. The only workaround at this point is to save before the first encounter, then stasis the hunter in a spot in the room that makes it so when you do enter a safe area, they freeze far enough away from the doors that you can go around him. Otherwise, you reload the save and try again. Until they patch it, this is the only thing I know of that for sure works. I've heard that if the hunter leaves the room and then you enter a safe area, the glitch won't happen, but I've not yet tested this so I'm unsure if it works yet.