Unity Reload Scene - References missing / objects inactive upon reload

When playing the active scene, all the references are linked through inspector like the game manager

However, when reaching a simple game over and pressed the restart button, all the references (like the game manager) are missing despite that all of the objects are tucked away under the same scene I am reloading.

I remember encountering a similar question about references, but the answer seems to be unclear except for DoNoDestroyOnLoad, which is not what I want to do. nor does it solve the problem of missing references. Is there any way that I can reload the level EXACTLY like the first time? Without having to use a lot of "DoNotDestroyOnLoad".

Link to similar question without clear answer. http://answers.unity3d.com/questions/1373722/keeping-reference-after-scene-reload.html