Make a bootable CD then!
Lots of versions of Linux will do whatever you want with your disk partitions for the cost of a blank CD.
Similarly there are lots of sites with free boot disk utilities.
Why will the 98 disk not do it? Is it not bootable?
AFAIR, 16-bit DOS will delete NTFS (i.e. non-DOS) primary partitions - it's only extended partitions it has a problem with.
SD