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DNS Zones missing on old DC after upgrade from Windows 2003 server to windows 2008 server

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We have a network with two servers, an SBS 2011 server and an SBS 2003 server that we are migrating from. The migration is almost complete but we have run into replication problems with AD between the two servers. All the FSMO roles have been successfully transferred over to the new server before the replication problems started. Almost everything has been moved over from Exchange except for a few public folders that failed to replicate properly.  We have a full backup of the 2003 server from before the migration but we don't have one from after the migration before the problem occurred.

The local DNS Zone is missing in DNS on the 2003 server (both the domain.local zone and the _msdcs.domain.local.  We are unsure how it went missing. It was there and now it is not. I can get AD replication to work from the 2003 server to the 2008 server but AD replication does not work from the 2008 server to the 2003 server.  I get the following error:  The target principal name is incorrect. I assume this has to do with the missing local zone on the 2003 server.

I need to uninstall exchange and properly demote the old server but do not want to do this before I resolve the replication problem (not sure it will allow me to do it in any case until I get it fixed). I know that the exchange uninstall cleans up AD as part of the migration process.  Would also like to pull the remaining public folders over as well but I can always get those out of the backup if I have to and restore them manually.

I have set security for zone transfers in the DNS zones on the new server to Nonsecure and secure and have set an allow for transfers to the IP of the 2003 server.

I have attempted to registerDNS and start and stop the netlogon server on the 2003 server but the zones will not populate. 

Any idea how can I get the local zones back on the 2003 server so that I can get replication going again?  Can I just uninstall DNS and the re-install it?  The error in DNS on the 2003 server is Event ID 4000 - The DNS server was unable to open Active Directory.  I am also seeing 4013: The DNS Server was unable to open the Active Directory. this DNS Server is configured to use directory service information and can not operate without access to the directory.  The 2003 server is set to refer to itself for DNS with the 2008 as a secondary. AD seems to work fine, at least I can access it on both servers, it is just the replication and DNS that seems to be broken.

I have to shut the 2003 server off during the day or I get authentication problems with Outlook on user's PCs because the Information Store will not start on the 2003 server (I am guessing this has to do with the AD / DNS issue.  I can only turn it on at night to work on it.  Any ideas you might have would be appreciated.

Thanks,

Dave


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