Steps to repro:

1. Open the attached project.
2. Run REPRO/Bake menu item. Assets\White\Scenes\mainmenu_base will be generated with bake data.
3. Clear GI cache.
4. Close Unity.
5. Start a new Unity instance and create a new project.
6. Close Unity.
7. Copy over the entire Assets folder from the repro project to the newly created empty project.
8. Open the newly created empty project and let everything import.

OR

1. Load attached project.
2. Run REPRO/Bake menu item
3. Close Unity.
4. Delete Library\metadata files
5. Load project again.

Expected result:
Bake data copied from another project is consistent with initially baked one.

Actual result:
Errors:
"Lighting data asset ‘LightingData-1’ is inconsistent because 3 files out of 67 are missing. Please use Generate Lighting to rebuild the lighting data." warning message.
are shown meaning that copied lighting data is different from the initially baked one.
See attached screenshot.
Regression introduced in Unity 2017.1.2p4.

Notes:
- Reproducible in 2018.2.0a1, 2018.1.0b4, 2017.2.1p3, 2017.1.2p4;
- Not reproducible in 2017.1.2f1.