I changed some directives in the virtual hosts by hand, but they suddenly disappeared.
Never edit the vhost file manually. On the next update of the system your changes will be overwritten! Instead put your additional vhost configuration in the Apache Directives field in the ISPConfig Interface.
If you want to add something manually to other files, e.g Postfix' local-host-names, you can put your configuration at the end of the file in a section that is not overwritten by ISPConfig.