FindObjectsOfType HideFlags.DontSave problem

Hi, I'm currently making a level editor in runtime and I want some instantiated items to remain after it has finished running. I currently do this by using HideFlags.DontSave and because of that they stay in the scene after returning to the editor, which is perfect.

However if I use FindObjectsOfType to collect the at the start of a new session, the script can't see them, returning null. If I just place the prefab I use in the hierarchy normally it works just fine. Does anyone know of this issue or has another approach on keeping instantiated gameobjects in the scene after runtime?