Even back in my super noob days, I'd keep known good working versions of the files in separate folders. I basically invented my own terrible source control system before I knew anything about svn or git.
Looks like they weren't staged. He clicked on the staging option, it showed it would stage thousands of files, he said "hey I should fix my .gitignore" and clicked on what looked like either a "don't stage" or a "forget" button, and it was a "checkout --force" button.
The most impressive thing is all the people doubling down on the idea that a "checkout --force" button in a main interaction screen is a great idea, there's nothing wrong with the software, and the user is a moron.