I would advise you going for the hard painful way.
Think about it this way, today you manage to do a little voodoo on your music folders, and you kinda get it where you want to. But as time goes by this clusterf''k of files really gets out of hand. Then you'll be redoing this another time and another, etc...Without really felling the beneficial part of really tidying your library.
I say do it right, it will be painful, and it will be a very long process.
What i can offer with what i gather from the way your files are organized :
-backup your entire library onto an external hard drive,
-create two new folders, one called "dj set", the other keep it as "my music",
-inside "dj set" create several folders depending on the type of electronic music (if you only play house go for subgeneras, like electro house, classic house, vocal house, etc..).
-then, and there is no real way around, painstakingly move your music from your "master music folder" to the "dj set", one by one, over the course of several months (yeah i know).
-keep djiing the way you used to (with the way it was organized) until your are about 30/40 % in the process.
-at this point, point traktor to only read and update from your "dj set" folder.
-when prompted at analyzing your collection for missing files, just delete the missing, you'll have almost started anew.
This is a painful process but very important, doing this you will get you around to listen to a lot of tracks to decide wether or not to keep them, check if the quality is good enough, or if you need to trash it and buy a good quality one, etc...
Because too much music is detrimental to doing your thing (at least if its a real mess), the only way to be able (in a sane fashion) to handle a really big music folder, is by having it organized.
I hope i didn't sound patronizing or anything
I had to do this process once and it took me almost a year, but now when i add music to my library, tagging 10/20 files a week, getting the name, file structure, everything nice, clean, and most importantly in a productive manner is really easy.
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