When you install Windows 2000 to a new folder or partition on an existing Windows 9x system for dual booting, Windows 2000 Setup modifies the boot sector to load the Windows 2000 boot loader at boot. The boot loader gives you the option of booting either Windows 2000 or Windows 9x depending on the selection you make from the boot menu, which is defined in the Boot.ini file.
If you decide that you no longer want to use Windows 2000 on the computer, you can keep the system as it is by deleting the system folder but continuing to use the boot loader to boot Windows 9x. A cleaner solution, however, is to remove all Windows 2000 files, including the boot loader.
Create a boot disk
To remove all Windows 2000 files, boot the computer to Windows 9x and insert a blank, formatted disk into drive A. Then, open a DOS prompt and execute the SYS A: command.
This command copies the system files to the disk so you can use it to boot the computer to a DOS prompt. You can also format the disk through the GUI and choose the option to copy the system files to it to create the boot disk.
Remove the Windows 2000 files
Next, copy the files Sys.com, Format.com, and Fdisk.exe to the disk. Boot the computer using the disk, and then execute the SYS C: command.
This command overwrites the existing boot files and restores the Windows 9x boot loader. Then, you can remove the Windows 2000 folder and the boot files Ntldr.exe, Boot.ini, Ntdetect.com, Arcsetup.exe, and Arcldr.exe from the computer. If Windows 2000 is installed in a different partition, use Fdisk to remove the Windows 2000 partition or use Format to reformat it for use with Windows 9x.