Yes, take it down. Shut it down, power it off, close it or make it crash. I don't know the exact reason of the servers being "down" or "gone" from the MP server list, but everyone was kicked out and some of the servers restarted (automatically I suppose) setting up the mission that was being played, and others completely disappeared from the list.
I do not own a server, I just play MP on any server available with good ping and this has happened on different servers with different missions (wasteland, hold position, TDM, co-op, etc)