I've encountered a rather unfortunate issue.
Soooo, here's the deal. I've installed a few mods since the other night when I finished a mission in which I lost a couple characters. At the time everything seemed normal. But as I come back into this campaign I can see that all of the resistance contacts have disappeared, and I mean every single one. All the ones I've contacted and every one I haven't.
The mods I installed really shouldn't have affected anything that deeply. They were either new weapon mods or cosmetic mods. I fear that when I replaced the MoreCities mod with the ISky Updated List mod that I may have somehow altered my game irrevocably, but I'm just not sure. I'm troubleshooting now, but if anyone else has had this happen to them, please, let me know what you ended up doing.