Scene Setup - Inventory System Manager and Item Object Spawner Script issue

I have went back through the instructions again and they do say to do the scene setup on each scene I have in my game. When I do this, and save the scene, and I go to load the next scene what I just did gets deleted on the previous scene. I have checked and my Game Objects that are already in the game arent prefabs, I didnt do this with them since each of my levels needed greatly different game objects. So what am I doing wrong? It works fine in level one. I guess I could try to mark the one on level 1 to Do Not Destroy on Load but then I still dont have the Item Object Spawner Script moving with it.

*While writing this out I thought of a solution. Im manually adding those two scripts and setting them as needed and that is working. Not sure why the Scene Setup Add Components would add them but then not let me save the scene with the newly added scripts. *I even tried to change something in the scene to get the asterisk to pop up stating I could save. When I clicked the Scene Setup button the save asterisk wouldnt appear at the top like no changes were made. Again this object wasnt a prefab. I hope this helps someone.
 
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