How can I find an OSX application that is running but whose window is not visible?

Open AppleScript Editor and insert the following script code, replacing Safari by your application's name:

tell application "System Events"
    tell process "Safari"
        repeat with wnd in every window
            set position of wnd to {40, 40}
        end repeat
    end tell
end tell

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Check System Preferences » Displays if you have multiple displays connected (could be virtual) and whether a button Gather Windows is available. Click it.

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You could also try Mercury Mover, a software that allows you to control window movements using the keyboard.

I encountered a similar problem once when playing with Multiple Displays. I resolved it like this:

1. I reduced the resolution of the display to a resolution lower than my current one causing the window to be auto re-positioned onto a visible portion of the display
2. I dragged the window to a different position;
3. I switched the resolution back to the original one showed the window.

You can find the display settings at:

• System Preferences -> Display -> Resolution
• Changed to Scaled -> Selected a lower one (e.g. select 1344 x 490 down from 1440 x 900)

Select the application. From the application window select zoom. The window should be visible on the screen. From the application window select zoom again to set the size of the window as previously defined.