I may be misunderstanding what you're asking for here... But couldn't you just update the tags with a command line tagger residing on your Empeg? Just mount your music drive RW and do something like this pseudo-code:

foreach fid file ending in 1 (ascii "tag" files)
do
grab fields from fid (title, artist, comment, year, genre, etc)
pass them onto command-line tagger, passing the corresponding *0 FID's filename
done

If I knew of such a command-line tagger (I'm CERTAIN they exist) I would recommend one. Maybe others do... I know the shell script to do this couldn't possibly exceed 10 or 15 lines.

Any problem with this strategy? The MP3's would be edited in-place on the Empeg, saving the long and difficult journey from Empeg to PC and then back to the Empeg.