I don’t know why, but at one of my servers the domains.list file gets erased every x weeks. So after some weeks they are missing in the httpd.conf and the domains will not work.
Before I figure out what causes it, this is a little piece of code to fix the list and rewrite httpd:
for d in `ls /home/user/domains`; do echo $d >> /usr/local/directadmin/data/users/user/domains.list; done /usr/local/directadmin/custombuild/build rewrite_confs
