Why don't project window changes persist after a crash?

For example I changed one of my prefabs attached scripts prior to a crash I just had. The prefab is not in scene, it’s in the project window, on the disk. Why doesn’t a change to a file like that persist after a crash? After reloading my project and hitting start I get a null reference error because the script isn’t on the prefab. I also lose shader tweaks and other public variable changes that aren’t related to the scene.

Is that the difference between the “save project” and “save scene” options? Does “save scene” automatically call “save project”? I hit ctrl+s all the time, it just seems like a crash will still wipe out certain changes. Thankfully crashes are few and far between for me, but I don’t understand why files on disk revert to their previous state.

Sometimes (usually) we skip over the easy stuff. Written pretty plainly in the manual though.

“To save changes to the scene, select Save Scene
from the file menu, or hit Ctrl/Cmd + S. This saves current changes to the scene and Does a “Save Project” (below).”

I guess I just hadn’t ctrl+s’d in a while because I wasn’t working on scene data.