I know it's dumb to make a issue for suggestions but theres no other way, you should add like a panic button and a load saved (If you press panic it all turns off but it makes a backup of what you had example: iiMenu_SavedEnabledMods.txt, it would disable the mods which would cause the iiMenu_EnabledMods.txt to wipe itself. So when you press load saved it uses the iiMenu_SavedEnabledMods.txt to load it back which update the iiMenu_EnabledMods.txt.
I know it's dumb to make a issue for suggestions but theres no other way, you should add like a panic button and a load saved (If you press panic it all turns off but it makes a backup of what you had example: iiMenu_SavedEnabledMods.txt, it would disable the mods which would cause the iiMenu_EnabledMods.txt to wipe itself. So when you press load saved it uses the iiMenu_SavedEnabledMods.txt to load it back which update the iiMenu_EnabledMods.txt.