A. Microsoft does not support the upgrade of Windows 9x to Windows 2000 in a dual boot environment. The problem seems to occur if Windows 2000 is already installed on another partition. You may get the errors:

Windows 2000 Setup does not support upgrading from Windows if you have multiple operating systems installed. Setup will now exit.

or

Other Operating Systems Found

You cannot upgrade this Windows installation to Windows 2000, because you have more than one operating system installed on your computer. Upgrading one operating system can cause problems with files shared by the other operating system, and is therefore not permitted.

To official solution is to uninstall the other Windows 2000 installation and remove the files ntldr, ntdetect.com and boot.ini from the system partition (c:\). You can try to just delete those files and leave your other installation intact and once the Win9x upgrade is complete modify boot.ini to include a link to the existing Windows 2000 installation.