Ok I have here in my hot little hand a Western Digital IDE Hard Drive that has one big partition on it, set active and I need to make it non-active.
Currently the drive holds data and WIn98. The data needs saving and Win98 needs a burial at sea. The main drive has XP and is formatted in NTFS.

This lives in a Biostar M/B and the bios is set to boot "other" The WD drive is on the IDE2 bus as the slave. If you leave this drive in, the boot time is +5 minutes and Xp is your OS, if you Take the WD Drive out on the other hand the boot time is much faster. Fast is good!
With the bios set to boot "HD1" and both drives in the computer it boots WIN98 in a normal time for Win98. You dont "see" the other drive (SATA)

What Im hoping for is someone will have a hint or solution to fix this. When I showed this problem to Fdisk, it just laughed and laughed, and laughed.

Now granted I do have some options. Namely just dumping the data to something else and then firebomb the partition. Lather,rinse and repeat. However I was looking to something a bit more...elegant.