The template file used by dns rebuild zone function is:
/usr/local/cwpsrv/htdocs/resources/conf/web_servers/conf_templates/named_new_dns_zone.conf
and is different of the default zone template to create new accounts:
/usr/local/cwpsrv/htdocs/resources/conf/dns/bind/zones/default.tpl
create a new file, make a backup, on update should be overwrited.