Why isn't Unity allowing me to apply certain changes to a prefab?

Question

I have a prefab called square in the asset tray, I drag it into the scene to create an instance of the square prefab (in the hierarchy it is highlighted blue and has the select, revert and apply buttons in the properties). If I move/resize the instance and then press apply, the changes are applied to the prefab.

However, the square prefab has a script with a public game object. I drag the game object from the hierarchy into the slot in the instance's properties tab and is shows that the script is now referencing the actual gameobject. However, when I press apply this change isn't applied to the prefab (the prefab's script still isn't referencing any actual gameobject). All other changes to the prefab are applied.

I have tried dragging the instance into the asset tray to create a new prefab with the changes, but, as soon as I do, the script no longer references the game object.

I shouldn't have to create an entirely new prefab every time I add a public variable to a script so why can't I apply this change?

Answer 1

Ok you can't really drag an instance to a prefab. As a rule of thumb keep instances with instances and prefabs with prefabs. I would instead find the instance from the prefab when this one is instantiated, with a method like findobjectoftype, or gameobject.find. Let me know if you want me to expand the answer

Answer 2

Solved: Prefabs can only reference other prefabs since there might not be an instance. Made the actual gameobject into an instance of a prefab and applied the prefab to the script

Answer 3

Prefabs are Assets. You can reference only other Assets to an Asset, never instances of Assets.