So I know why it is happening, but did not expect that.
When you delete object from the level, and that object has a reference in the SaveGameFile, the reference on that object will be renamed to “None” in random time, could it be 10 seconds, it can be 1 minute. When you destroy it and quit the game, it will stay saved. So my brain is telling me that this is somekind of a bug I found out. But probably I am missing something 
I did not think that this could be a problem, when you Save the variable, you saved it. I understand that Objects are already created instances of class. But … why?