This is utter nonsense. If you're currently running a machine that has any version of Windows on one partition and Linux on another partition, you can overwrite the Windows partition when installing Windows 2000 and just leave the Linux partition alone. These operating systems coexist quite nicely. The one thing to watch that is Windows 2000 likes to take over the PC's master boot record and displace LILO, but a reinstallation of LILO after Windows 2000 is configured addresses that issue. This technical posting from Microsoft reeks of fear.
Misinformation is one thing, but technically incorrect misinformation is another.
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