This took a little while to nail down, but it seems that ScholarLy's
annotation engine fails silently when \RemoveEmptyStaffContext is
active.  Almost-minimal example attached.

Is there anything I should be doing differently?

And should I be filing ScholarLy issues here or on the openlilylib list?

-- Graham
\version "2.19.21"

\include "openlilylib"
\useLibrary ScholarLY
\useModule scholarly.annotate

#(display "Scholarly loaded\n")

\setOption scholarly.annotate.export-targets #'("plaintext" "latex")

\score {
  \relative c'' {
    \time 2/4
    g4 g g g g
    \musicalIssue \with {
      message = "last note, A. bar 3"
      context = "Some staff"
    }
    NoteHead
    g
    \break
    R2*3
    \break
    g4 g g g g g
  }

  \layout {
%{ %Toggle this block comment to reveal problem:
    \context {
      \RemoveEmptyStaffContext
    }
%}     
  }
}
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