So I have a FSM that I'm using as a placement script for my game where it has a transparent object that follows your cursor and then when you place the object it destroys it's self and creates the right object. The game object that it places is a variable that is available in the inspector. I've made some new prefabs to replace the place holder objects, which are also prefabs, but it seems every time I close unity and open it back up it reverts back to the first game object that I assigned it. I can open different scenes and it keeps the right game objects assigned to the variable.