You could give your Server processor priority on your PC in hopes that a random event like a virus scan wouldn't cause such an issue again. Details on How: Open Task manager find your running server under "Processes" tab (probably just Java as MC runs in java) right click > select "go...

I've had this issue before, but don't remember exactly what I did to fix it.
I would try:
-updating or downgrading your Java.
-Reinstalling the mod on a fresh server jar.
-Start the server with more memory (http://minecraft.gamepedia.com/Tutorial ... p_a_server)

I've had ghasts disappear and reappear later when moving horizontally in the world, but when the ghasts go too high vertically they seem to vanish forever. I never go chasing them to check and see if they are just up in the sky unloaded or something...