I've installed Linux Mint 19.1 with the Mate desktop.
When I click on the minimize button on any window, the window disappears and I can't find how to return it to the screen.
Any running process, such as copy, will continue to run.
I had similar issue (or perhaps the same issue). When I had several instances of a program open (firefox, for example), when minimized I could no longer get all of the instances to open back up when clicking on the task bar/panel/system tray. In addition, the nice preview screenshots did not pop up when I hovered over the icon in the task bar/panel. The instances can still be accessed by using Alt+Tab keystroke. Guided by Kaleb, I:
I'm sure a full "Reset Panel" could work but if you have any custom settings, they might be lost.