Well, I was thinking, maybe in windows simple "shortcuts" may be created rather than making a physical copy of the file. Those may be detected by emplode so that it could recreate the "link" when copying mp3s back to the empeg. Shortcuts (*.lnk) also work well under windows command line, at least in Win2k/XP (which is not dos! In dos they would not work!), but after all if you're using emplode that means you are using windows.
Actually, NTFS always had a symlink featiure that is not very well known (the best way to use it is to dload the free utility JUNCTION.EXE from SysIntrnals), which works more or less the same way as under unix, so that could be used too, but maybe using .lnk is simpler.