The default apache VHOST created with the one-click app (/etc/apache2/sites-available/000-default.conf):

<VirtualHost *:80>
        ServerAdmin webmaster@localhost
        DocumentRoot /var/www/html

        <Directory /var/www/html/>
            Options Indexes FollowSymLinks
            AllowOverride All
            Require all granted
        </Directory>

        ErrorLog ${APACHE_LOG_DIR}/error.log
        CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>

In here you can see the site root is at /var/www/html . This configuration and this directory is being handled seperated from all the other VHOST’s with different roots.
As long as you create your own new directory for your new website as explained in the tutorial it won’t affect your current site since its root is somewhere else.
In the tutorial you will also create a new VHOST for the new website, since this also doesn’t affect any configurations from your current site; nothing will happen.
You don’t need to reconfigure anything and you can execute this tutorial as many as you like as long you don’t affect the other sites with directories/VHOST’s.

Hope this makes it a bit clear.