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I do believe that you can do this from within 2000 itself without the need for fdisk (see my post on fdisk).
If you wish to keep the harddrive in 2 partitions, then just format the partition and remove the boot entry in boot.ini.
The 2 OS's are seperate and don't communicate with each other so they wont complain if one is "missing"
And if you do wish to merge the partitions "diskpart.exe" or partition magic is your best bet, since if you are using windows2000 your filesystem is most likely in ntfs and therefore fdisk will not be able to merge the partitions
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