Depends.
Which of your partitions are set as active?.
What are you using for booting?lilo?
If so, lilo could be on the mbr ( in which case, its ok to wipe out your Linux partition). Or linux could be in your root partition and that partition may be set as active/bootable.
On a ordinary Win98/Linux sys., I'd just recommend "fdisk /mbr", but you have Win2K as well. At any rate, just setting the active partition as your "C:" partition usually suffices.
Need more info for specific advice.
Ciao
-khorgath