Seems that template files now are unused, due to that config had changed to be made at database level.
Check youself, acessing the phpMyAdmin, database 'root_cwp', table 'settings', fields 'apache_vhost_tpl' and 'apache_sub_vhost_tpl', have a identical configuration of that template files.
This is an example of the problem of CWP developers, failing to publish a changelog.
We simply don't know what was changed, at least in features, and if you have customizations, you are lost.
Regards,
Netino