Faça um backup primeiro :) E então tente o truque de atualização / reparo no local, ele deve funcionar bem em 2000.
Confira Resgatar uma instalação do Windows 2000 com uma atualização no local para mais informações.
Insert the Windows 2000 CD into the drive, restart your system, and boot from the CD. Once the initial preparation is complete, you’ll see the Windows 2000 Professional Setup screen:
To initiate the in-place upgrade, press [Enter] to launch the Windows 2000 Professional Setup procedure. When you see the License Agreement page, press [F8] to acknowledge that you agree. Setup will search the hard disk looking for a previous installation of Windows 2000. Once it finds the previous installation, you’ll see a Windows 2000 Professional Setup screen:
When Setup locates the previous installation, you’ll be prompted to initiate the in-place upgrade.
As you can see, this second screen prompts you to press R to repair the selected installation or to press [Esc] to install a fresh copy of Windows 2000. In this case, initiating a repair operation is synonymous with performing an in-place upgrade, so you’ll need to press R.