Hey, the_qrv,
Presumably, your add-in's script was initially packaged up in a .jmpaddin file along with an addin.def file and possibly an addin.jmpcust file, is that right? Your best bet, especially if you are distributing this add-in to others, is to take the updated script along with the original addin.def and addin.jmpcust files, assuming they have not needed to change, and zip the files back up into a .jmpaddin file (which is a .zip file whose extension has been changed to .jmpaddin). When you (or others) open that .jmpaddin file in JMP, JMP will ask you if you want to re-install the add-in, and if you say Yes, JMP will write the new version of the add-in files over the old ones.
Hope that helps,
Eric