After editing website configuration using ISPConfig 3, under Sites tab > website, the vhost file created by ISPConfig was reset automatically to it's default value. All the custom config that I added was lost. Example I set the following line to: Code: server_name mysite.com www.philnews.ph; root /var/www/mysite.com/web; index index.php index.htm index.html index.cgi index.pl index.xhtml; Now, when I update the site "mysite.com, the vhost reset to default like: Code: index index.html index.htm index.php index.cgi index.pl index.xhtml; Notice the php file will move again to the 3rd location. Note that this happen to anything that you change in the web domain config like changing the password of "Webstatistics" under statistics tab. How to prevent this?