Kalecgos to add to askvortsov Flarum itself (through normal usage or through command line commands) might override files in the public/assets and storage folders, but it should be pretty evident which files that might be since it's either log/cache files, or CSS/JS/images provided by extensions and their names are generally prefixed or very predictable.
Some extensions might copy additional resources into those folders as well.
Adding additional images, HTML files or other special files for SEO/identification in the public folder is generally safe since it's unlikely an extension will override those specific filenames.
The Sitemap extension could cause an externally generated sitemap.xml file to be overridden for example.