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I understand.  The next time you are in 'Extended' mode you have to manually move all the panels back to monitor 1 though.  Why not have a '1/2 display' toggle that switches and remembers settings for both cases?  Or put the main image in its own window and allow users to move it to the second display, like PS does.
Just a suggestion, not criticizing your fine piece of software, which I like a lot.