I think we might all be a little lost as to what you're actually trying to do still.
So I'll start trying to be helpful, though I don't have Excel 2000 to actually try it on.
Typically, from an app within Windows, the open or save dialogs will call an API that will open the file system folder for Documents as specified in the registry.
In Vista/7, it would be C:\Users\CurrentUser\My Documents
In XP it was C:\Documents and Settings\CurrentUser\My Documents
So, if you have hard set references from to other files in the folder, I can see how that'd break it and it'd not be a version thing at all.
The folders can be moved around if you really want to. Basically My Documents is a folder that is tracked by the system, and it really doesn't care so much where it is on the filesystem. It's supposed to create a little more separation of the top level GUI of finding your docs vs. where the stuff is actually stored, so in theory you don't have to worry about it.
To change the location, go to Start, click on your username on the right hand side of the pane at the top, and you'll see your user folders. (This also assigns proper security to the view, so it shouldn't lock you out)
From there you can right click on My Documents, and it should have a location tab. From the location tab, you can move it and force it to be in the old location if you really want it to.
I'm not sure if that'll really fix the problem though (since I'm not really sure about what the problem is and what the command prompt has to do with it), so more details would be good.