For anyone else looking for how to do this, I didn't think to look in the generated version file:
# ATTENTION!
# DO NOT MODIFY THIS FILE OR ANY PART OF IT. THIS CAN RESULT IN IMPROPER PLESK
# FUNCTIONING OR FAILURE, CAUSE DAMAGE AND LOSS OF DATA. IF YOU REQUIRE CUSTOM
# MODIFICATIONS TO BE APPLIED TO THE CONFIGURATION, PLEASE, PERFORM THEM IN THE
# FOLLOWING FILE(S):
#/var/www/vhosts/domain/conf/vhost.conf
#/var/www/vhosts/domain/conf/vhost_ssl.conf
and then run
$PRODUCT_ROOT_D/admin/sbin/websrvmng --reconfigure-vhost --vhost-name=domain.tld
Original thread here: http://forum.parallels.com/showthread.php?t=108936