How do you save a reference to a prefab's script in a ScriptableObject?

So, I have a ScriptableObject class called "Template" that stores a reference to a script on a Prefab. You can see it here: http://i.imgur.com/qjfJ4eA.png

It's the first field, the "TileMarker". That script is located here, on this prefab: http://i.imgur.com/VszE3v0.png

And here is the inspector view of that prefab, showing the "TileMarker" script: http://i.imgur.com/G42qmCj.png

Notice that the "TileMarker" script also has a field that points back to the "Template" which is the ScriptableObject. So, this all works fine until I save the project, exit, and come back. For some reason, the "Template" loses its reference to the "TileMarker" after saving and exiting: http://i.imgur.com/zoysakN.png

Strangely enough, the "TileMarker" doesn't lose its reference to the "Template". Only the ScriptableObject pointing to the Prefab's script loses the reference. The prefab script pointing to the ScriptableObject is fine. Is this a quirk of ScriptableObjects? Can they not store references like this permanently? Is there a way to work around this?

Thank you very much in advance for any help you can give.