...Do you guys even know how patches work?
Patches check the difference between two ROMS (the edited and unedited ones) and make a patch that will edit the part of the ROM that has been changed in the edited one.
So, if you have a ROM that has a script at 800000 and another with a script at 400000, if you create a patch that patches one of the ROMs onto a clean FR ROM and patch it onto the other, both remain. However, if you create a patch for one over the other, then only one script remains.
Did you get all that?
...Or, well, I think that's right.