Steps to reproduce:

1. Open attached project "Lights.zip"
2. Open scene "B"
3. In Lighting tab make sure that Precomputed Realtime GI is enabled and build lights
4. Open scene "A" and runt it. Objects look like expected (not overexposed)
5. Build and run project
6. Notice that objects are overexposed

Additional steps:
7. In editor, open build settings
8. Make scene "B" as primary (drag it to the top of the list)
9. Build and run project
10. Notice same result as in editor

Reproduced with: 5.3.3p1, 5.4.0b8
Not reproducible: 5.2.4f1