Prefabs loose connection to scene object

So I am trying to use EditorUtility.ReplacePrefab(), but when I select scene objects they become missing when I reenter play mode. I noticed I can select Prefabs in the assets and used GameObject.Find to set it to a scene object at the start, but this isnt really ideal. Is there a way to keep the connection/reference to the scene object? Thanks for your help.

No, that’s not possible because prefabs are assets and they can’t rely on objects in a certain scene.

When you instantiate the prefab, what would you expect when the scene with the referenced object isn’t loaded?