In this case, the .htaccess file in the parent directory (www.example.com in this example) will also affect the subdirectory (es.example.com). If 6Scan is installed on the site in the parent directory, its modifications to the parent .htaccess may affect correct operation of the site in the child directory.
To fix the problem, create an .htaccess file in the child site's root directory (/usr/home/example/www/es/ in this example), which contains the following single line:
RewriteEngine On
This will cause the parent site's.htaccess to be ignored by the child site, preventing any problems.