\header {
  title = "Different instruments for different scores"
}
\paper {
  scoreTitleMarkup = \markup { \column {
   \on-the-fly #print-all-headers { \bookTitleMarkup \hspace #1 }
    \fill-line {
      \fontsize #3 \bold \fromproperty #'header:piece
      \fromproperty #'header:opus
    }
    \fill-line {
      \fromproperty #'header:instrument
    }
  }}
}

\score { 
  \context Staff << { c'1 | R1 } >>
  \header{ piece="Piece 1" instrument="Instrument 1"}
}

\score { 
  \context Staff << { c'1 | R1 } >>
  \header{ piece="Piece 2"
           instrument="Instrument 2" }
}