It doesn't remove custom httpd-ssl.conf, if it's setup in /usr/local/directadmin/custombuild/custom/ap2/conf/extra/ (official method).
Regarding TLS v1.1 - maybe /usr/local/directadmin/custombuild/custom/ap2/conf/ is the reason, if there is something inside?
Regarding TLS v1.1 - maybe /usr/local/directadmin/custombuild/custom/ap2/conf/ is the reason, if there is something inside?