Please please PLEASE... do not save your changes in the standard Mach4 profiles (i.e. Mach4Mill, Mach4Lathe, Mach4Router, etc.). As you have found out, they WILL get overwritten when you install a different Mach4 version. Open the Mach4 Loader, select the profile then click on the "Copy Profile" button.
Likewise, if you have any custom changes to the screen set (custom buttons or Lua code), copy the screen set to some other name. I'm not in front of a PC with Mach4 at the moment, but from the screen editor I think it is something obvious like "File->Save As" (or *some* menu then "save as").
Bob