How to reproduce:
1. Open the previously-attached project in Unity
2. Open testScene
3. Select TestObject in hierarchy and notice that prefab assigned to a scipt is none
4. Switch to your Explorer or Finder application, open the project's
directory, and move the Update folder into Assets
5. Switch back to Unity and let it import the new assets. Do NOT use
"reimport all" and do NOT reload the scene.
6. Create an empty GameObject in the scene.
7. Choose "File > Save Scene."
8. Select TestObject in the scene and notice that the prefab assigned to the script is still none

Expected: TestObject has references to TestPrefab

Workaround: in step 5 use reimport all or reload the scene and you will not have this issue

Simpler reproduction steps:
1) Open the scene.
2) Dirty the scene by adding an empty game object.
3) Save the scene.

Notice how the reference to the TestScene.prefab (6457997b0d824be43acf47d8a741c32d) is now gone from the scene file.