If I was to manage this today
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I will use engine dj (desktop) directly with external drive.
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I will have one Parent folder containing all the subfolders you mentioned
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I will drag this Parent folder to Engine DJ collection. Engine DJ automatically will create all the subfolders in the playlist tree.
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Engine DJ will analyse and do it’s thing
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If i add new tracks to some subfolders, I will delete the main folder in Engine Playlist tree and drag the Main folder again.
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Step 5 does not remove tracks just the playlist