I don't think there is a way to remove them, aside from using just *one* single 'menu channel {' instead of two.
Yes I know this can be a hassle.. but it's the only real way to deal with it..
example, your first menu channel { } is located in one.mrc, and the second one is in two.mrc, you could remove both menu channel { }'s from there and then use:
menu channel {
Utilities
.$iif($script(one.mrc),My Tool1) :/dosomething
.$iif($script(two.mrc),My Tool2) :/dosomethingelse
}
This may not be the best way to deal with it.. but if you know the script is loaded and know that the menu is in there no matter what, then you can use something like this, and just comment out the old menu channel { }'s.