This is still a problem in Natty, although the behavior is somewhat better.
If I have two or more horizontal virtual desktops (in ccsm, General Options -> Desktop Size -> Horizontal Virtual Size), then when disabling a monitor to the right or left of my primary screen, windows on the disabled monitor get moved to one of the other virtual desktops. Similarly, if I have two or more vertical virtual desktops, then when disabling a monitor above or below my primary screen, windows on the disabled monitor also get moved to one of the other virtual desktops.
However, if I have only a single horizontal virtual desktop, then windows on a disabled monitor to the left or right of my primary screen are still lost. And similarly, if I have only a single vertical virtual desktop, windows on a disabled monitor above or below my primary screen are lost.
This is still a problem in Natty, although the behavior is somewhat better.
If I have two or more horizontal virtual desktops (in ccsm, General Options -> Desktop Size -> Horizontal Virtual Size), then when disabling a monitor to the right or left of my primary screen, windows on the disabled monitor get moved to one of the other virtual desktops. Similarly, if I have two or more vertical virtual desktops, then when disabling a monitor above or below my primary screen, windows on the disabled monitor also get moved to one of the other virtual desktops.
However, if I have only a single horizontal virtual desktop, then windows on a disabled monitor to the left or right of my primary screen are still lost. And similarly, if I have only a single vertical virtual desktop, windows on a disabled monitor above or below my primary screen are lost.