When working with multiple screens and many workspace windows, sometimes if you minimize one of them, it gets "lost" (you cannot see the minimized square at the bottom). Usually this gets solved by minimizing and maximizing the main FlexSim window and then the other windows will reappear.
It would be good to have a collapsable menu (maybe in the View Tab) where you could see all the current open windows in the workspace and bring them to view from there.