To reproduce:
1. Set up perforce external control system.
2. As a root workspace use users attached project (in zip file New Unity Project folder).
3. Open Unity and open this project.
4. Disable auto refresh in Edit->Preferences
5. Update prefab file and script in perforce client ( use new prefab and script from folder Assets_FromPerforce)
6. Switch to Unity and make refresh.
7. Notice that prefabs second value is set to scripts value (70) but not to prefabs assigned value (2)
8. Restart Unity
9. Notice that prefabs second value is set to correct value (2).

To reproduce without even using Perforce or other version control system:
1. Open the "New Unity Project" project in Unity.
2. Disable auto refresh in Edit->Preferences
3. Overwrite the folders located in the project directory with the ones from Assets_FromPerforce.
4. Switch to Unity and refresh the Asset directory.
5. Notice that prefabs second value is set to scripts value (70) but not to prefabs assigned value (2)
6. Restart Unity
7. Notice that prefabs second value is set to correct value (2).

Reproduced on: 5.4.3f1, 5.5.0f3, 5.5.2f1, 5.6.0f3

Not reproducible with new prefab workflow: https://unity3d.com/prefabs