Comment 13 for bug 1244397

I just stumbled across another way to regain control of the missing windows. Right-click on the X11 dock icon and select options->"Desktop on Display N" where N is the index of one of your displays. Clicking on the correct one of these will eventually bring all the windows for inkscape into the same display and the missing one will appear again.

Moving windows around can still make them disappear again depending on where the focus is but this does at least allow you to get hold of the missing one without resorting to unplugging the second monitor...