If it's the system partition, you can't remove it.
You can backup your reg and create the ERD by going to;
Programs|Accessories|System Tools|Backup, then choose ERD, then if you check
the box for "Also backup....", then the reg will also be backed up to
%windir%\repair\RegBack
leaving the
%windir%\repair\
directory files intact as original installation.
If you format the partition, then you'll need to boot the recovery console
and from a command prompt issue the command;
fixboot
To start the Recovery Console, start the computer from the Windows 2000
Setup CD or the Windows 2000 Setup floppy disks. If you do not have Setup
floppy disks and your computer cannot start from the Windows 2000 Setup CD,
use another Windows 2000-based computer to create the Setup floppy disks.
Press ENTER at the "Setup Notification" screen. Press R to repair a Windows
2000 installation, and then press C to use the Recovery Console. The
Recovery Console then prompts you for the administrator password. If you do
not have the correct password, Recovery Console does not allow access to the
computer. If an incorrect password is entered three times, the Recovery
Console quits and restarts the computer. Once the password has been
validated, you have full access to the Recovery Console, but limited access
to the hard disk. You can only access the following folders on your
computer: %systemroot% and %windir%
Also before hand create a boot disk. For the floppy to successfully boot
Windows 2000 the disk must contain the "NT" boot sector. Format a diskette
(on an NT machine, not a DOS/Win9x, so the NT boot sector gets written to
the floppy), and copy ntldr, ntdetect.com, and boot.ini to it from the root
of the system partition. Then boot the floppy to test.