Reproduction steps:
1. Open the attached project "case_1362344.zip"
2. Open the "SampleScene" Scene
3. Duplicate this Scene
4. Open the duplicated Scene and delete the "Sphere" GameObject
5. Open Lighting window from Windows > Rendering > Lightning
6. Set Lightmapper to Progressive GPU (Preview)
7. Set Min Bounces to 2
8. Set Max Lightmap Size to 2048
9. Press on Generate Lightning and then save the Scene
10. Open the "SampleScene" Scene
11. Observe the "Sphere" GameObject
Expected result: "Sphere" GameObject Material stays the same as before
Actual result: "Sphere" GameObject Material is black
Reproducible with: 7.7.1(2019.4.30f1), 10.6.0(2020.3.18f1), 11.0.0(2021.1.20f1), 12.0.0(2021.2.0b11, 2022.1.0a7)