MacBook Air with jumbled up directory

A couple of months back, a friend of mine has purchased a mac air (13, 2017). Suddenly he was unable to see a drive icon when an external disk was attached in on the left side usb port and thought the port had a problem. Actually, when I looked at the system I found the directory structure was completely jumbled up. The main folders (Document, Download, Macintosh HD etc) were distributed here and there and did not even show up in the Finder. But they are all there. Would it be possible to get back the correct directory structure by reloading OSX? The user directories may be moved to different disk and reloaded into the system after directory repair. I forgot to mention the system OS is High Sierra. Any suggestion with be highly appreciated. Thanks a lot.