Hi,
This is the basic principle of a Prefab. Editing the prefab itself will affect the entire project and all instances of this prefab. Editing only an instance of that prefab is only local and do not affect the rest of the instances nor the original prefab.
I would NOT/NEVER edit a single instance of a prefab, this is dangerous and never really what you want. Instead prefer, implement a more complex fsm to handle a special case or have a new prefab if the feature is so different.
Saving iterations of your work is best done using a repository like GIT or SVN. I would not start duplicating your prefabs to keep track of things that would pollute your project files for no real benefit.
bye,
Jean