Demoting a win 2000 server with a win 2003 server on the same subnet

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I have two domain controllers with different domain names but on the same subnet and with active directory installed. One domain controller is win 2000 and the other is win 2003. The computers are in a workgroup the users don't log on but are connected to the win 2000 box with shares to a program. If I take active directory off the win 2000 box and demote will that affect the computers that are In a workgroup connected to the shares? I want to install all the programs and shares on the new win 2003 box but one computer win not let me log on to the win 2003 box it says no domain available. What can I do to slowly migrate the programs and shares to the new server?
 
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