Greetings
Okay I'm comming in a bit late, But... If I understand the Question You want to convert the System/Home partition for win2k to NTFS, Without loosing anything, right?
Go to the DOS/Command Prompt (I'm assumeing Win2k's on C
and type convert C: /fs:NTFS
Press enter
It willgive you a message that says "Can't do this while Windows is running ,would you like to proform conversion on next boot? y/n"
Hit Y
Press enter
reboot
enjoy!
I did this on a Win2k Server yesterday
Stoic Joker