If the option is enabled, DA will search that server to see if the zone exists. If it does, it will give the "domain exists" message as if the zone existed on the current machine, preventing the user from creating the domain, or you from creating the user.
If you move accounts to a different machine, then you'd need to make sure that the option is not checked during creation (on machines that share the NS), or if it's the machine that is holding the duplicate, then you'd need to make sure the zone isn't on that machine. If you first delete the account from the server you're moving from, then there won't be any issues (understandably, not always an option).
The checker can only go so far, and it becomes a balance between
1) preventing users on other machines from creating duplicate domains your duplicate zones.
and
2) allowing you to move accounts around.
The "checkbox" should be the balance for you. If you want to flexibility, just uncheck it, and DA will blindly write to other machines, so your zones get duplicates correctly.
I'd recommend keeping the both checked, or none at all during normal operations. When moving accounts, I'd recommend keeping them both unchecked. Once the move is done (assuming users didn't conflict with any zones locally), then you can re-check them, and issue a full rewrite of all dns zone (echo "action=rewrite&value=named" >> /usr/local/directadmin/data/task.queue) and DA will at then transfer everything over.
We may need to add a "remove all zones" button, so DA will remove zones from a remote server. Once complete, you can add them again. We'll see what's needed in upcoming releases.
Thanks for the angle though
John