First, always use source control so you can trivially revert when weird stuff happens.
To solve this you’re going to have to track down what’s going on, either by disabling stuff, twiddling lighting settings, chopping parts out of this scene and putting it in a different scene, trying to isolate what is going on. It might just require a simple re-bake of the lighting.
“Use source control or you will be really sad sooner or later.” - StarManta on the Unity3D forum boards
Personally I use git (completely outside of Unity) because it is free and there are tons of tutorials out there to help you set it up as well as free places to host your repo (BitBucket, Github, Gitlab, etc.).
You can also push git repositories to other drives: thumb drives, USB drives, network drives, etc., effectively putting a complete copy of the repository there.
As far as configuring Unity to play nice with git, keep this in mind:
Here’s how I use git in one of my games, Jetpack Kurt:
Using fine-grained source control as you work to refine your engineering:
Share/Sharing source code between projects:
Setting up an appropriate .gitignore file for Unity3D:
Generally setting Unity up (includes above .gitignore concepts):
It is only simple economics that you must expend as much effort into backing it up as you feel the work is worth in the first place.