Deduplication of tracks currently only works within a single playlist. If the tags match, then the file is discarded as a duplicate.

This is recursive -- you can drag the root of your music directory from the PC to the root playlist on the empeg, and it should "just work".

This doesn't work for deduplicating across the entire player, and the tags are a little restrictive -- meaning that you can't change the year, for example, without the file on the PC not being spotted as a duplicate.