mIRCs internal protection list is not related to the remote's state. It's stored separately.
Remote files are what they are called: additional "aside" code to do "custom" things - e.g. the above remote script is for manipulating the protection list (of mIRC) if the script is running, and will stop doing this if you turn your remotes off or unload the script.
Thus, the very moment you turn your remotes off you'll halt processing of the remote script (and all other remote scripts), is not processed further, and the protection list will remain in it's current state.