I may not have been as clear as I could have been; I'm not concerned about what I consider a legitimate duplicate. (In a Box Set, and on the original album.) As far as I'm concerned, the vast majority of that 10k+ list is not a duplicate. It's the 50 to 100 that are in the "Separates" folder that are the potential duplicates. Drive space is cheap, and I use my folder structure to differentiate between Original albums, live albums and Compilations within my playlists.
My previous Media Manager had a method to show me a list of duplicates where one of the duplicates met some specific criteria. For Example; If I had a track in Separates, that was also on two other albums, the list would show all three tracks. If I had another track which is on three different albums, but none in "Separates," none of those would show on the list.
Since I continue to get new music all the time, and I add new music to the "Separates" folder constantly, I would rather have this a bit less cumbersome, than sorting through a fresh playlist every time I get new music. I'm hoping for a way to streamline my process to; "add and tag albums, check my custom playlist, remove real duplicates from separates, and then auto-organize to the appropriate location." I also had some auto-playlists I could make from this; based on number of entries for the title in the database, tracks with at least 3 starts that only exist on regular albums, Tracks that don't appear on any compilation, and one of my favorites; songs with the same title, from all artists.
I hope that makes sense to you. It sounded perfectly understandable in my head, but I'm not sure it all went out through my fingers.