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You can follow these steps to do a inplace upgrade (without the
inplace problems)
1. install another BDC (on a temporary computer)
2. Promote it to PDC (using Server manager)
3. Upgrade the newly Promoted PDC to Windows 2000
4. Install another 2000 DC (Join existing domain)
5. Transfer the FSMO roles, Licensing Server, and GC to server in 4.
6. Remove the old PDC
7. Install a second 2000 DC