Reproduction steps:
1. I used this simple project, that's on GitHub https://github.com/UnityCatalina/bug/invitations
2. Open the project on machine 1and leave it running
3. On machine 2, clone it and change a simple Graphics setting (e.g. change the Lighing from Linear to Gamma)
4. Push that change
5. Back on machine 1, pull that change while the project is still running
6. Notice the shadows going all black and the lighiting is yellow (see attached screenshot).
7. Try to re-bake lighting, and notice it doesn't improve it. Also, in Unity 2018.1 0b8, the colors of the framework change (see attached screenshot).
8. Reloading the whole project fixes back the lighting

Same steps yields a correct lighting result in Unity 2017.3 0f3

Please check the attached screenshots to see the lighting difference.
While the example project is very simple, I have encountered this issue during Scenario Test Week with a scene that had the Post Processing Stack on it. All the effect of the PP are turned off when this issue occurs. It DID occur really often especially at the start of the project, when a lot of us were changing project settings.