When I set up a headless client on my server and then start the mission and disconnect the mission continues to run and any future connections count as JIP with all the same vehicles, wrecks, AI, corpses, etc. still in the mission. This is despite the fact that I have the dedicated server set to not run the mission persistently.

I strongly suspect that this is caused by HC's counting as players. I'm not sure if HC's counting as players has any benefits for scripting, but I know it causes a lot of problems such as this one and one I found while searching: https://feedback.bistudio.com/T83864