are you kidding? Using Partition Magic to remove a HPFS partition?! That's not true, is it? This is like driving into town for shopping with a 40-ton monster truck! Now, be serious:
All you need to do is run DOS fdisk:
So, if the Win98 CD is bootable: Boot from that CD, select "start from CD", next "start with CD support" (not the actual Win setup that's to say). Then run fdisk (by entering "fdisk"), answer "Y" if it tells you anything about large disks and you're presented with the fdisk main menu.
If you're having more than one disk drive, make sure you have selected the right one (the one that contains the partition to be removed) with option "5". ( If you're having only that one disk, there's no option "5" )
Once the right drive is chosen, select "3" for remove, then "remove non-DOS partition", and enter the number of the partition shown in fdisks table. Done.
If that doesn't help, you can try to run "fdisk /mbr" which (re)creates a new master boot record.
If that doesn't solve the problem, you still can run OS/2 if it's still bootable, press ALT-F1 when the "boot blob" appears in the upper left of the screen (the small square and "OS/2"). Then choose to boot into an OS/2 command prompt, run OS/2's fdisk (by entering "fdisk") and remove the partition.
If that doesn't work either, tell us if you have an OS/2 CD and/or the install floppies, so that we can explain you how to get a bootable OS/2 in order to access (and to remove) the HPFS partition.
If all fails, you can still try to "force corrupted partitioning data" by changing the IDE disk type in BIOS so that it doesn't recognize anything on the drive anymore. Run fdisk to create whatever partition (that'll kill the old partition table), then reboot, enter BIOS and re-set the correct drive type.
Now you're ready to boot DOS, run fdisk on the drive and you're done.
And only if all this fails, you might need a copy of partition magic.