I'm not sure if its a glitch or something happened but here's my situation
I gave my npcs a load out and let them patrol. A few months pass and then I noticed that almost all if them are missing there load out button that appears when you kook at their squad details. I've checked my items and it says that they are equiped to the bpc.
That happens to mine when I update their Fitout while they are patrolling. Perhaps that's what happened to yours. They come back when I stop them, and give them the appropriate items to carry. Then I send them patrolling again.