Saving reference to a ScriptableObject with JsonUtility

I have a data structure like the following

     [Serializable]
     public class InventoryWrapper
     {
         public CardInventory[] Data = new CardInventory[0];
     }
     [Serializable]
     public class CardInventory
     {
         public CardDefinition Definition;
         public int Quantity;
     }

CardDefinition in the example above is a ScriptableObject class. I'm using the JsonUtility.ToJson and JsonUtility.FromJson functions to save this data structure to disk and loading later. It appeared to work fine and generates output as follows:

 {
    "Data":[
       {
          "Definition":{
             "instanceID":377496
          },
          "Quantity":2
       },
       {
          "Definition":{
             "instanceID":377502
          },
          "Quantity":2
       },
       {
          "Definition":{
             "instanceID":-2897598
          },
          "Quantity":2
       }
    ]
 }

This morning all my references broke and when the data is serialised FROM JSON I get null objects instead of references to my ScriptableObjects. Am I going about this in the wrong way? Can anyone help