Scripting

I have an application thats been deployed already. However I need to change the permissions on some HKLM reg keys of the deployed application. I'm treating this as a patch. I exported the reg keys in question and imported them in to a blank ism. I then changed the permissions of the keys in my new project. I installed the patch over the app and almost all permissions were reset as requested, however some keys were not reset. Is there any other way to modify reg key permissions????:)