I use EFF and Convenient Horses, and lately I've been having this problem where my followers attack my supposedly friendly and essential horses and I can't get them to stop.
They stand there, slashing at the air, while the horse stands there doing nothing. I can't talk to them, and I don't think EFF has an option like AFT and Vilja do where you can command them not to attack whatever they're attacking.
Stopcombat, unfortunately, doesn't help. They immediately unsheathe their weapons and go back to attacking the horse.
Best Answer
Try the Followers Stop Fighting Each Other mod.
It stop followers fighting each other, although it should work in your situation. Good luck!