So did you solve your problem? If not, have a look on the following code
below:

\version "2.17.28"
\relative c' {
  \override Stem.transparent = ##t
  \override Flag.transparent = ##f
  \override Beam.transparent = ##f
  f16 f f f \autoBeamOff f16 f f f 
}

By what I understand, making the Stem transparent also changes the Flag and
the Beam, so you need to manually set their transparency to ##f

Regards,
Gilberto



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