As of 1.33.7, DA can do this without needing to change your httpd boot script:
http://www.directadmin.com/features.php?id=980
Older manual way:
If you want to avoid download interruptions during apache restarts, apache has to be changed to restart gracefully.
To do that, you'll need to change your httpd boot script.
The path for your script will vary depending on your OS.
For FreeBsd it's:
/usr/local/etc/rc.d/httpd
For all other OS's, it's:
/etc/init.d/httpd
As for the actual change, you'll edit the httpd boot script for your system, find this code:
restart)
stop
waitforexit "httpd" 20
start
;;
restart)
kill -USR1 `cat $PIDFILE`
;;
An apache restart will no longer start apache if it's stopped. Â You must "start" it, as the graceful restart only works on already running processes.