It sounds like you're attempting to restore the IIS 5 Metabase to a different Windows 2000 system. Microsoft states that this won't work becuase the metabase backup/restore are not intended for disaster recovery purposes, nor for replicating IIS configuration. Your best bet is to restore the content, and manually reconfigure the IIS settings.
Regarding your problems with the DNS files, I think your solution is as simple as deleting the EnableRegistryBoot value from the registry key located at HKEY_LOCAL_MACHINESYSTEMCurrentControlSetServicesDNSParameters. You can replace the DNS files immediately after installation; however, if you use the DNS Manager to create and administer zone files, the EnableRegistryBoot setting is created and the registry is considered to be the correct source. The text files you want to work with are no longer used. Of course, if you make this change, any zones you have created with DNS Manager will be lost.
So, if you haven't created any zones with DNS Manager, go ahead and delete the EnableRegistryBoot setting, replace the files, and restart your server. If you can't afford to lose the zones you have created, you'll have to manually add the information from your DNS files into the DNS Manager.
This was first published in June 2001