I think updating is always a problem when using 3rd party module-scripts, that is probably the reason.
Not sure if there is a good fix for this.
I suggest you do it like I described earlier.
Perhaps putting all 3rd party module-script in the RetroPie-Setup/ext directory like this :
/home/pi/RetroPie-Setup/ext/<3rd-party-repository-name>/scriptmodules/<supplementary|emulators|etc>
will make updating easier just cutting and pasting only the ext directory in the new RetroPie-Setup.