I created my local site in my projects folder that looks like this:
/sites/project-name/version-2/
Inside of this folder I have all files related to my project, design files, content, etc. so the site’s path was:
/sites/project-name/version-2/app/public
I deleted the site via Local app and it deleted the Version 2 folder instead of the app folder. This means it deleted all of my project files. No big deal because it just moved them to trash, but I would assume you’d simply want to delete the app folder instead.