Repro steps:
1-Open the Bug scene.
2-Select the Bug GameObject
3-Link a reference to any UnityEngine.Object in the "Reference" field
4-Press the "Serialize" button
5-Save and reload the same scene
6-Press the "Deserialize" button
7-Notice how the "Reference" field has changed - sometimes it gets empty, sometimes it references to absolutely different game object

Expected behaviour: after deserialization it references the same object
Actual: serialization drops after reloading the scene

Reproduced on: 5.4.0b21; 5.3.5p3;
No EditorJSONUtility on 5.2 and earlier