1) Down the two BDCs prior to upgrading the Windows 2000 server. This will allow you to have a backout plan with a clean NT 4.0 domain should you have to go back.
2) After the Windows 2000 Upgrade is done on the NT 4.0 PDC you created, you will want to delete the references to the old BDC's in the Active Directory before you add the two new Windows 2000 Servers with the same names.
After that, things should work out well.
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