No, changes to VirtualHost will not be preserved. Those changes need added to /usr/local/apache/conf/userdata/std/<apache version>/<user name>/custom.conf
The file doesn't actually need to be named customer,conf, as long as it end with .conf
After adding such a file, run:
Code:
perl /scripts/ensure_vhost_includes
once that is done, the Include directives will be added to the vhost and retained across httpd.conf regenerattions.
On a side note, there is a bug in 17046 (Current and Edge) that causes the httpd.conf be regenerated by anything that modifies the httpd.conf. Thus, adding a subdomain will cause the entire file be regenerated. This will be fixed in the next build.