Hello there,
I have tried twice now, but when on Windows, with Unity 2017.2.0f3, deleting the library folder, ruins my project.
When i delete that folder, and try to start my project again, it will indeed rebuild some things, but several things will be missing, and the project is unusable. am i doing something wrong?
The scene is empty when i load the project after deleting the Library folder. When i undelete it, everything works fine again.
It is true, that when you open up your project after deleting the Library folder, it opens an “Untitled” Scene, because it doesn’t know, which scene to open…
But if you manually choose to open your “Game” scene (or whatever you called it, when you saved it), then everything reappears and the project works, at least, it did that for me. 
Glad i’m not the only one that was having this issue. thanks @ShadeWolfDK for the explanation, it really helped.
I have the same issue. Even when reopen my game (as suggested above so the hacker terminal console assets appear in the Scene window) it still causes my game to not run. The console appears but none of my script is running. Some cursory debug prints don’t run, Terminal.WriteLine isn’t working, nothing appears to be connected.
I can only get it to run by restoring my library.