So, very weird issue that I couldn't find a Google solution for. While I had thought it was something weird happening with Knockout and Surrender - the issue persisted even after uninstalling it and cleaning the file.
Long story short: NPCs that are meant to die in scripted events - such as Skjor during the Companions questlines - just don't. They enter the Bleedout state and can't be interacted with in any way. In vanilla this isn't really an issue - since the questlines continue like they nothing went wrong and I can just disable those that refused to die. It's annoying but it is what it is.
The issue is when certain modded quests (Vigilant, in this case), need said NPC to be dead to trigger things such as removing a barrier that leads to the next area. I've tried various console commands but they don't work. I ended up no-clipping through the barrier to get to the door and and, but still...
While I'm certain it's me being a dumb-dumb somehow (it usually is) - I was wondering if anyone else has encountered this issue, and what they did to fix it if they did?