It sounds like you’re not source controlling properly.
All meta files MUST be committed properly or Unity will make new ones and mayhem results.
PROPERLY CONFIGURING AND USING ENTERPRISE SOURCE CONTROL
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:
I usually make a separate repository for each game, but I have some repositories with a bunch of smaller test games.
Here is 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 the ONLY folders you should ever source control are:
Assets/
ProjectSettings/
Packages/
NEVER source control Library/ or Temp/ or Logs/
NEVER source control anything from Visual Studio (.vs, .csproj, none of that noise)
Setting git up with Unity (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. Digital storage is so unbelievably cheap today that you can buy gigabytes of flash drive storage for about the price of a cup of coffee. It’s simply ridiculous not to back up.
If you plan on joining the software industry, you will be required and expected to know how to use source control.
“Use source control or you will be really sad sooner or later.” - StarManta on the Unity3D forum boards
SCRIPTS OR ASSETS ARE MISSING OR BLANK
Some info about Missing script warnings, broken prefabs, GUIDs, renaming GUIDs, etc:
EVERYTHING in Unity is connected to the above GUID, which is stored ONLY in the metafile, and hence why the metafiles ALWAYS MUST be source-controlled.
When Renaming: It is super-easy to inadvertently change the GUID by renaming outside of Unity. Don’t do that. Instead:
close Visual Studio (important!)
rename the file(s) in Unity
in Unity do Assets → Open C# Project to reopen Visual Studio
now rename the actual classes, and MAKE SURE THE FILE NAMES DO NOT CHANGE!
If you are NOT using source control while you do this, renaming files is an EXTREMELY dangerous process. Use source control at all times so that you can trivially revert if you miss a critical step and damage your project.