It only works if you copy the MNS into two separate folders, so that each version can create its own MNC/MNR files. It means you have to maintain two files, but at least you can just copy & replace one of them when you make a change. Then the MNC/MNR files will recompile and you'll be all set again.
So now I have a "Menus\AutoCAD" folder and a "Menus\AutoCAD LT" folder, with the same MNS in each, and everything's fine.