I've had a response back from Unity, and its a bug that hasn't yet been fixed (even in 2019)
https://issuetracker.unity3d.com/issues/prefabs-references-are-lost-when-modifying-prefabI have been trying various workarounds to try and get a different solution - but as it stands, the rebuild works correctly but in scene references get broken due to the above. Anyone desperate for a fix - I would recommend importing our temp fix, but it still causes major issues (i.e. you need to reload the scene to see changes) as of right now.
Edit: I should add they are not broken, but they are broken in the viewport and in the inspector until the scene is reloaded, or a script recompile is triggered... Net result = not a great result, but its not broken.