The way our phpMyAdmin installation works is simply that it’s installed in /var/www/phpmyadmin and then we symlink to that directory from your web root. If you have lost access, this probably means the symlink was removed. You can fix this by running the Change Web Root tool and just leave the web root entry as-is – this will recreate the symlink – or you can execute the following command (if your web root is /var/www/html – modify accordingly):
ln -s /var/www/phpmyadmin/ /var/www/html/phpmyadmin