# echo "action=rewrite&value=named" >> /usr/local/directadmin/data/task.queue
# echo service named restart
where of course the # simply means you run the command as root; you do not type the #.
But you can't regenerate nonexistent zones with this command, as it simply rebuilds them in place from the standard or any custom template. I don't know if there's a command to do that or not.
However your update didn't delete any zones. It just moved them to a place where DA can't find them.
To fix the problem you need to change your copy of BIND back to non-chroot. To do that first comment out the last line(s) (which set the chroot for BIND) in /etc/sysconfig/named.
Then make sure that both /etc/named.conf and /etc/named.conf.rpmsave have all the necessary zone file lines in them.