When we are working on some project, there are always some Objects we just created once and duplicated multiple times without setup a Prefab.
After a couple weeks, for some reason we want to update that old object. We will figure out that a small change you will need to do about 10 or 100 times, because we don’t want to break the object dependency and everything is just duplicated there without using any prefab.
This tool is something like the remedy method to help you convert the scene object to Prefab Instance.
How to use:
- Select multiple object
- Right click > Convert To Prefab > Convert Window
- Pick your base object
- Convert!
Good tools can save your time, hope you have a nice day. 
Store Page:
A Tool when you forgot to Prefab (GameObject to Prefab Instance) | Utilities Tools | Unity Asset Store
For the Version after Unity 6.0 is using Unity method ConvertToPrefabInstance to Convert Prefab Instance, everything will just work fine with keepig Object Dependency and Merge different Object as Possible
For the Version before Untiy 6.0, I used a different way to implement feature, I used other way to implement and keep object dependency as possible (It is not the Obsolete method ConnectGameObjectToPrefab ). In this version, the most of the case can work fine and Keeping Object dependency. But be careful for the Nested prefab, if object inside the Prefab is referenced by object outside the Prefab, object dependency will still be broken