Ubuntu deletes itself?

[CommanderLiamTHX]

I installed Ubuntu on a computer, and it worked fine after I installed it, but the next day, I turned it on, and Unity crashed on startup. I installed the GNOME desktop, and it worked fine. I started it up, and it gave me an error. I booted off my original Ubuntu USB stick, and looked at the hard drive, and about 5 core folders were missing. Why did this happen? How do I fix it without deleting the files I put on this?

 

[Slacker]

I am not really an expert but if it was a fresh install how much will you loose just doing a fresh install? That said I am sure if you check out ubuntu forums or even hang out here there are a few experts that can tell you what folders to replace and how to.