Windows 2000 up to Windows 2003R2 create zones in CN=MicrosoftDNS,CN=System,<defaultNC>, samba joins such kind of domain and the Windows DC(s) are demoted there is no way to migrate the DNS zones to DNS partitions (DomainDNS & ForestDNS).
It would be nice to have a tool to allow the migration by copying records that are not up to date in the DNS partitions and then remove the container in CN=MicrosoftDNS,CN=System