Hi Kieren,

If they’re in the same file (which they appear to be), then I believe the MIDI 
output of your second \score block — the non-detuned one! — will overwrite the 
MIDI output of the first one. You need to have separate files (or at least 
separate \book blocks, with explicit and different target file names) in order 
to output two separate MIDI files.

I think you're mistaken:

\version "2.22.0"

music = { c' }

\score {
  \music
  \layout {}
  \midi {}
}


\score {
  \music
  \midi {}
}

generates test.midi and test-1.midi.

Lukas


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