Answer is negative. Unless I'm missing something. My loading class basically loads a buffer scene, then loads a cutscene, then loads the buffer scene again (thats where the code in my second post is being called), then finally loads the game. I have one GameObject that might be the culprit, and that's my Settings class, which is a singleton and is not destroyed between scenes. I need to try and test that out, maybe that's keeping a reference lingering. However, the odd thing is that all references are destroyed between scenes. So even if in the inspector it says "Missing", would that still keep an atlas from destorying itself, if that "Missing" reference is a gameobject with a class that is inside the atlas hierarchy?