Steps:
1. Open attached project (lpdemo.zip)
2. In menu: test > testTestLightMapParameter
3. In Hierarchy check Mesh Renderer component of
a)"Cube_Prefab"
b)"Cube_NoPrefab"
c)"Plane"
Note: Lightmap Parameter is empty on all of these GOs.
4. Save scene and reopen project
5. In Hierarchy check Mesh Renderer component of
a)"Cube_Prefab"
b)"Cube_NoPrefab"
c)"Plane"

Expected behavior: Lightmap Parameter is empty on all of these GOs.
Actional behavior: Lightmap Parameter of "Cube_NoPrefab" and "Plane" are set to "Scene default"; "Cube_Prefab" parameters stays as expected.

Reproduced with: 2018.1.0a3, 2017.2.0p1, 5.6.4p2.