Solution:

I just found a solution to my problem. The atom window was rendered outside any screen >coordinates. I did the following steps to solve it:

Alt + Tab to choose the atom window
Alt + Space to open the context menu
Press 'm' to select move
Press any arrow key once
Move your mouse (The misplaced window will follow your cursor.)
Open a new file or project and close it again to save the new window state.

originally found here atom/atom#6939