Hi there,
If you're planning on returning to the scene where you make objects DontDestroyOnLoad, you might want to consider copy-and-pasting the Easy Save 3 Manager to the other scene instead. You could also try to destroy the duplicate manager when you enter the scene, but I'm not sure how you would guarantee that it is deleted before the manager performs its own checks in Awake().
Just to clarify, Auto Add Manager to Scene simply adds the Manager to the scene. This doesn't guarantee that the dependencies of other scenes have been added to that manager, or that the dependencies have the same instance IDs. So there was no way of the second scene of knowing that the ScriptableObjects existed. You might instead consider whether there is a way of creating the ScriptableObjects in the scene in which they're being used, rather than in the Main Menu. However, this very much depends on your project whether this possible, and the case may be that DontDestroyOnLoad is the only way in your circumstance.
All the best,
Joel