How do I restore my prefabs from my Git repository?

I have set up my Unity 4.0 project in a Git repository with the following gitignore:

.DS_Store
Library/AssetImportState
Library/AssetServerCacheV3
Library/FailedAssetImports.txt
Library/ScriptAssemblies
Library/ScriptMapper
Library/assetDatabase3
Library/cache
Library/expandedItems
Library/metadata
Library/previews
Library/guidmapper
Temp
*.pidb
build

I was working on a bug in my scene, and I decided to go back to my last git commit with git checkout. However, after doing that, two of my prefabs (they were pretty complicated with nested objects) disappeared from my scene and now they appear as white boxes in the Prefabs folder in my project. Why did this happen, and is it possible to restore them in any way?

Like nsxdavid said, the whole Library folder should be ignored. Enable meta files if it isn’t already, update your gitignore to ignore the whole Library folder, then delete your Library folder, so that Unity will recreate it with the proper data set up. You’ll probably want to reset to some earlier commit where things were still ok.

And backup everything first, in case things get worse.