Create a copy of /usr/local/directadmin/data/templates/named.db at /usr/local/directadmin/data/templates/custom/named.db.
In the latter, make any of the changes you want.
There's a command you can send to the task.queue which will cause all the zone files to be rewritten to the new template, but unfortunately I can't remember it or find it right now .
All or nothing for the task.queue commands, but if you just want to do 1, the go to Admin Panel -> DNS Administration -> domain.com -> and click "Delete" without selecting anything. That will rewrite just the 1 zone.