The computer was just running something called chek disk, it just checks your hard drives for errors and corrects them. It doesn't delete any of your documents or anything. If your computer is running this a lot, and your files/documents/folders are disappearing and/or your computer is freezing or showing a blue screen and restarting a lot then your hard drive is for sure going bad on you and you NEED to backup whatever you want to save before you do anything else at all. Because that hard drive could die on you entirely in a matter of hours to weeks.
You can download a program called HD Tune for free, and run diagnostics and tests from the program to check the health of your hard drive. I would recommened backing up your data before doing this because this will put the hard drive under stress, and could cause it to fail if it is already going bad on you.
So, your laptop was actually doing something to preserve its health and functionality...It's something that should be run on occassion, especially if you are experience minor issues. Just like defragmenting the hard drive and other maintenance tasks. A computer is like a car, it needs its equivalent of oil changes