I use Simplify3D 4.1.2 and Windows 10.
I doubleclick a .factory file in a filer.
And Simplify3D opens with the factory file.
And I override the factory file by Ctrl+S.
But a file dialog opens to save as.
If I open a factory file from the menu in Simplify3D, Simplify3D can override the factory file without a file dialog.