You want to perform an offline defrag of the Active Directory DIT to reclaim whitespace in the DIT file.
188.8.131.52 Using a command-line interface
Performing an offline defragmentation of your domain controllers can reclaim disk space if you've deleted a large number of objects from Active Directory. You should only perform an offline defrag when (and if) this occurs, e.g., following a spin-off. The database will reuse whitespace and grow organically as required. Typically, the database grows year over year as more objects are added, so the offline defrag should be seldom required. An offline defrag always carries a small element of risk, so it should not be done unnecessarily.
You might want to consider doing an offline defrag after the upgrade to Windows Server 2003. A new feature called single instance storage for security descriptors can greatly reduce the amount of space your DIT requires. With this new feature, unique security descriptors are stored once regardless of how many times they are used, whereas in Windows 2000 the same security descriptor would be stored individually on each object that uses it.
The key thing to plan ahead of time is your disk space requirements. If you plan on creating the compacted copy of the DIT on the same drive as the current DIT, you need to make sure that drive has 115% of the size of the DIT available. If you plan on storing the original DIT on the same drive, you'll need to make sure you have at least that much space available.
16.12.4 See Also
Recipe 16.2 for booting into Directory Services Restore Mode, Recipe 16.7 for checking the integrity of the DIT, MS KB 198793 (The Active Directory Database Garbage Collection Process), MS KB 229602 (Defragmentation of the Active Directory Database), and MS KB 232122 (Performing Offline Defragmentation of the Active Directory Database)