Before I try and answer, I want to be sure I understand the problem.
You click Edit to open Gradient Editor, but no editor appears. At the same time the main Inkscape window (canvas, tools, etc) gets unfocused. Next you say you can't see or click that window -- which window can't you see or click, the main Inkscape window or the Gradient editor window?
By unfocused, I usually think of a window being....sort of grayed out. I can still see it, but if I click on it, it becomes active (focussed).
What Inkscape version and operating system? In older versions, sometimes the dialog would become hidden behind the main window, when the main window was activated.
I'm not familiar with double monitor setups. I suspect it could possibly be contributing to this problem, even though only one monitor is on. But again, I'm not really familiar. Are there any special settings (in Inkscape Preferences) that you've had to make, to use the double monitor? If so, you could try disabling that. Otherwise, I'm not sure
There's also the possibility it's a bug, and some one else will comment on that, if so. (need to know version and os, please)
The Gradient Editor is one of the few dialogs which can't be docked. Normally, docking the dialogs can prevent them from "getting lost", but since this one is not dockable, that won't be a solution in this case.