In reply to:

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Often a song appears multiple times because it's included on a CD Single and on the album and on a soundtrack etc etc

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Exactly. If they are genuinely different versions (live vs studio, for instance), then I'll want to keep both. Otherwise, I generally keep the more "definitive" version (studio album beats "greatest hits" compilation beats mixed compilation), toggle coloured on the existing one, and replace it one at a time.

It's this last stage I'd like to automate.

I just spent quite a while replacing about a dozen instances of the 4-minute radio version of American Pie with the full-length one (the hard bit was where I had it in a playlist for recording onto cassette for empegless trips - I had to make an extra 4 minutes of space for it).