To convert a UNIX system to a Windows DNS is not too difficult. You set the Windows 2003 server DNS up as a secondary zone. Then you point to the UNIX DNS as the primary. You allow the Windows server to do a zone transfer. Now you have all of the DNS information on Windows. Convert the zone to primary. Then, dcpromo the machine to a domain controller. Finally convert the zone to an AD integrated zone. All of the DNS information that was on UNIX will still be there.
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