In the Unix world, files starting with a dot / period are considered "hidden" files. They are not normally shown unless when you specifically want them to show up in the directory listing. This in particular affects FTP programs. When you upload a file starting with a dot, e.g. the most popular one is called .htaccess, you may think it has disappeared because your FTP program does not show hidden files.
Most FTP programs provide the option for you to show hidden files, so you can see the files starting with a dot.