|I take it that you have win98 and winxp installed in a dual boot configuration?|
If that is correct, then your win98 will be installed in a FAT/FAT32 partition in the primary partition of your hard drive and known as the C: drive. Is this so?
Your XP will be installed in another partition either on the same drive or another drive and will have its own drive letter (more than likely this will be D:).
If the above assumptions are correct, then the boot files for both your OSes reside on the Win98 partition i.e. drive C:
Look at my website (link below) and look at the procedure to "KEEP WinXP and REMOVE Win9x":
☺ When everything else fails, read the instructions.