There would be two ntds.dit files present in case on Windows server 2008
%SystemRoot%\NTDS\Ntds.dit - This is the Ad database used by the domain controller, which holds the values for a domain and replica of values for forest
%SystemRoot%\System32\Ntds.dit -This file is used while promoting a windows 2000 server to active directory. This is usually called the distribution copy of the database. This file allows you to run dcpromo on a 2000 server without having to use the OS CD. During promotion, the ntds.dit file is copied from %SystemRoot%\System32 directory into the %SystemRoot%\NTDS directory. Active Directory is then started from this new copy of the file, and replication updates the file from other domain controllers.
reference: http://technet.microsoft.com/en-us/library/cc961761.aspx
%SystemRoot%\NTDS\Ntds.dit - This is the Ad database used by the domain controller, which holds the values for a domain and replica of values for forest
%SystemRoot%\System32\Ntds.dit -This file is used while promoting a windows 2000 server to active directory. This is usually called the distribution copy of the database. This file allows you to run dcpromo on a 2000 server without having to use the OS CD. During promotion, the ntds.dit file is copied from %SystemRoot%\System32 directory into the %SystemRoot%\NTDS directory. Active Directory is then started from this new copy of the file, and replication updates the file from other domain controllers.
reference: http://technet.microsoft.com/en-us/library/cc961761.aspx
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