Steps to reproduce:

1. Open user attached project
2. Select "FileCopy / "New->Origin" " from the Editor dropdown menu at the top
3. Reimport "HelloWorldScript" on Windows or "Refresh" in hierarchy on Mac
4. Select "HelloWorld" prefab and observe "Ref Obj 3" field being "Null" value
5. Double click main scene to re-open
6. Select "HelloWorld" prefab and observe "Ref Obj 3" have "RefPrefab1" value

Expected result: New->Origin editor script copies HelloWorldScript and HelloWorld prefab from a folder in the project outside assets. With it comes the references for the object fields in the HelloWorld prefab. The reference is loaded and "Ref Obj 3" has "RefPrefab1" value from the start.

Actual result: Upon swapping the Script and Prefab files, they get loaded, but reference is not shown. (Although it's not lost. Prefab file has reference information inside)

Reproduced on 2017.1.0b2, 5.6.0f3, 5.5.3p1

Notes: 5.4.x just loses script reference upon reloading scene.