One thing you could do is create a Windows program that will find the title bar of the cmd window you are working in, and minimize it in that program. In Win32, you should use the FindWindow command to get the window handle, then CloseWindow to minimize it. Something like this completely untested program:
int main(int argc, char** argv)
{
HWND wnd = FindWindow(
NULL,
argv[1]
);
CloseWindow(wnd);
return 0;
}
In the cmd window, you can set the title for a specific line (to avoid ambiguities), and then pass this name to the program in your program:
C:\>title TitleOfWindowToMiniMize
C:\>minimizeWindow TitleOfWindowToMiniMize
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