Is Git hiding files on my computer?

I've accidentally created two branches for my Git repository: main and master, which I now need to merge. However, when using ls on the command line while checked into main branch, some files on my computer don't show up (files that don't exist in the main branch on GitHub). When I use git checkout master the files "reappear". But they must always be on my hard drive, so why are they hidden from view when checked into this one branch?