View the original community article here
Last tested: Sep 14, 2020
Yes, Looker won't delete files that it didn't create. While deleting a project in Looker may delete the local project directory and its contents, Looker doesn't delete the project's remote repo so files you checked into the remote repo should be ok.
However, avoid putting large files into the git repo, especially in project directories in the repo, as project directoriess and all their contents are replicated on disk for every user that has access to that project and enters dev mode.