In a customer project we had to move the DNS from NetWare 5.1 Server to OES2 SP1.
We didn't used the Migration GUI or the Novell Documentation.
The easiest and best practices way was the DNS/DHCP Console.
First, you must install the new server in eDirectory and create a DNS Server Object.
In the second step use the DNS/DHCP Console to select the new server and take it to the authorized servers.
Now you have to select the old server and delete it from the authorized server list.
Do this for all zones.
Quick and easy.
Disclaimer: As with everything else at Cool Solutions, this content is definitely not supported by Novell (so don't even think of calling Support if you try something and it blows up).
It was contributed by a community member and is published "as is." It seems to have worked for at least one person, and might work for you. But please be sure to test, test, test before you do anything drastic with it.