Comment 144 for bug 1292398

Usually we handle one configuration per displays combination. So if you plug your laptop in your TV, it will have the same configuration the next time you plug it in the TV.

But in your case, we wouldn't know whether you're modifying the current configuration, or creating a new one.

The only thing I would guess is that mutter (which loads and saves the configuration) doesn't remember the position of the display you turn off, dropping it from the configuration. It should probably include it in the ~/.config/monitors.xml file, with its previous position, even if disabled.

That way, re-enabling it would pop it back in the same location.