You can rewrite the MBR and it should not do anything to stop your from booting into windows.
Pop a boot disk in (98 one is ideal ;-) ) click here
Let the computer boot from the floppy.
When you come to the prompt A:\>
Type: fdisk /mbr
So you should have A:\>fidsk /mbr
Click ok and it will pause for a few seconds, its actually rewriting the MBR then when its finsihed, Restart.