I’m sorry you’ve had this issue. Please consider using source control in order to guard and protect your hard-earned work.
Personally I use git because it is free and there are tons of tutorials out there to help you set it up.
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 the right .gitignore file:
ONCE YOUR PROJECT IS SAFE AND IN SOURCE CONTROL… now you can experiment.
Reimport all, then build. Does it work?
Make a single scene with a cube and build it. Does it work?
Add that cube to your non-working scene in the build. Do you see it?
etc etc etc
ALWAYS USE SOURCE CONTROL!!!