Plesk warns you, emphatically, not to mess with the auto-generated conf/httpd.include:
# 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/yourdomain.com/conf/vhost.conf # /var/www/vhosts/yourdomain.com/<subdomain-name>/conf/vhost.conf
Believe them. As tempting as it is to just put your customizations into that, don’t. Plesk will overwrite that file if you’re not careful (and yes, I found out the hard way).
So indeed, put your customizations into conf/vhost.conf as it recommends. But just creating the file isn’t enough, you also have to notify Plesk that it’s there as described here, then just bounce Apache.
# /usr/local/psa/admin/bin/websrvmng -a
(Feature request for Plesk: create an empty vhost.conf by default and include it so it’s ready to go).