I'd posted about something similar a few weeks ago. Since then I've gone through and de-duped my media, reformatted the drive i have connected to my hifiberry, and copied everything over to it.
Going forward i'll manage changes to the media directory via rsync from my computer.
Is there a good way - once the rsync is complete - to have the hifiberry reindex the media folder without rebooting or umounting the USB drive (aka, can this happen in the background). I'll be doing this somewhat regularly as i add music, or update metadata on existing files etc...
I'd put together a script to push the music to the hifiberry and then kick off the re-index.