How can I re-name a prefab that is used in several scenes with many dependencies without breaking anything? Is it as simple as re-naming a game object or is there a way of making sure the links between it and its dependencies are not broken? I am using Unity version 2018.2.17f1
You can rename prefab in eny way anytime you like. Unity store links to any asset through asset GUIDs so name of prefab just not used by Unity itself. Just be sure you rename prefab inside Unity or rename coresponding *.meta file too.
You should be a bit careful though if you also use Collaborate. Renaming and moving files around can cause issues with it.
Good point. I dont use collaborate and dont have such issues. May be some one need to fire a bug to Unity that Collaborate dont support some core Unity features
@Jes28 Thank you. I will re-name it within the Unity Editor. Would it make a difference if I re-named the actual prefab itself (which is inside the Prefabs folder) or if I re-named the game object in the Hierarchy that is the latest and up-to-date instantiation of the prefab?
To say short Yes. Game object is not prefab, it is instance of prefab so you can rename it as you wish but this is not make any changes to prefab itself. And not break anything. Scene prefab instance just keeps reference to prefab itself using prefab id and additionally stores all property override that you do on instance. Base Unity concept is that you can rename anything because all links stored through asset guids.