You've probably reinstalled 2000 at some point, and told it to install to a second directory instead of overwrite the old directory (look to see if you have both a 'windows' directory and a 'winnt' directory). It's obviously taking up twice as much hd space, so, you probably want to get rid of one of them... problem is, you might not be able to tell which one is which on the boot screen... you'd need to boot into one installation, then go to the boot screen applet and see what directory it's pointing to... if you have the version that installed the boot loader, you'll see both boots... the other install of 2k won't have both installs listed. so, the one with both installs listed in the boot list is the dominate one... you could then boot up with a win9x bootup disk, run "fdisk /mbr" and get rid of the boot screen entirely... it should then simply load the install you discovered had the two bootups in the boot list. Then, ideally, you could just delete the other 2k windows folder. I say ideally, because there's a chance you've installed some of your software under the different system, so the driver/inf/config/reg files for that software might be in the other windows folder... Sorry for not being too specific, I'm not on my 2kpro system right now, so I can't give you an exact walkthrough.
So, it's a gamble really, and no matter what you do, it's a 'fix'. I think I'd simply reinstall w2k, and this time have it reformat the disk... of course, save everything you want to keep to a burned cd or something before doing that... but, I think that's the simplest and most effective solution in this case.