No. If you delete the partition in fdisk, it will just not show up in windows.
Your best bet would be to move all your important data over to the "E" drive. Start the computer with win2000 disk in and start the installation.
When it gets to the point of which drive you want to put 2000 on, delete the "C" and "D" drive. Then rebuild them as one "C", finish the installation.
The draw back with this is, that you will format the "C" drive and loose everything.
but it is an option.