Considering my case, when I change the configuration of any site that affects the virtual host configuration (.vhost), the only file that is in the "sites-available" (domain.com.vhost) is updated, the file located in folder "sites-enabled" (100-domain.com.vhost) it stays the same when that was generated. For the record, I have identified the problem when I change the IP domain and include an SSL certificate. *Sorry for my english The version of my ISPConfig: 3.0.5.1 / CentOS 6.4
in sites-enabled there is a symlink which points to the file in sites-available. If both are files in your case, then the symlink must have been replaced with a file e.g. when you edited it manually or copied it as ispconfig never creates a file in sites-enabled folder.
