Anytime you edit an asset (such as FBX) you expose yourself to the program renaming (or re-ordering or re-parenting) that asset internally. When meshes and materials magically go missing, this is very frequently the source cause.
Also, unless you configure the project properly to use visible meta files, you risk running into loss of data when you go deleting the Library folder.
I’m sorry you’ve had this issue. Please consider using proper industrial-grade enterprise-qualified source control in order to guard and protect your hard-earned work.
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:
https://discussions.unity.com/t/736093/3
Here’s how I use git in one of my games, Jetpack Kurt:
https://discussions.unity.com/t/807568/3
Using fine-grained source control as you work to refine your engineering:
https://discussions.unity.com/t/826718/2
Share/Sharing source code between projects:
https://discussions.unity.com/t/719810/2
Setting up an appropriate .gitignore file for Unity3D:
https://discussions.unity.com/t/834885/5
Generally setting Unity up (includes above .gitignore concepts):
https://thoughtbot.com/blog/how-to-git-with-unity
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.
“Use source control or you will be really sad sooner or later.” - StarManta on the Unity3D forum boards