I never got around to using mp3tofid myself, however...

If I remember right the symlinks were made on the computer to avoid duplicating the collection. Once those links are made, you ignore the source mp3 files, and use rsync aimed at the symlinks to the empeg.

There may be specific flags needed on rsync to ensure it treats the symlinks as full files instead of trying to replicate the symlinks to the empeg.

Aha, there is more details on the rsync steps Pim took with his personal setup in the readme. His project was migrated to GitHub by other members of the community here a few years ago. Give this a lookover and see if it helps: https://github.com/empeg/mp3tofid/blob/master/README.html