I've run into some odd behavior in LilyPond. If your PDF-only is a score but your MIDI-only is a separate book, the PDF file gets "-1" appended to the file name. So for instance, with this code:
%%%
\version "2.25.6"
theNotes = { c'4 4 4 4 }
\score {
\new Staff \theNotes
\layout {}
}
\book {
\score {
\new Staff \theNotes
\midi {}
}
}
%%%
...you get two files, one called "test-1.pdf" and another called "test.midi". The work-around is to use \bookoutputName and name one of the files something other than "test", but ideally I would want "test.pdf" and "test.midi" as file names.