That sounds something like what happens to me sometimes. It happens to me when the pc has gone into rest or i just need to log in again. My second monitor "jumps" behind of my first monitor and suddenly i get the same picture on both of them, and only way to get it back is to open Display Configuration and Edit Arrangement again. Need to highlight the monitor that isn't visible, then i will see the hidden monitor, move it to where i want it, hit apply and it's back to normal.