Try writing three staves, one for the part in unison, and one for each of the parts when they are different. Put full bar rests where the the other stave should be read.
Something like this:

Then use \RemoveAllEmptyStaves
to french the score.
To get something like this:

See the following code:
\version "2.19.83"
\paper {
left-margin = 15
}
%% Recorders One and Two
recorderOneTwo = {
\new Staff \with {
instrumentName = \markup { \center-column {" " "Recorders" " "}
\center-column { 1 " " 2 } }
shortInstrumentName = \markup { \center-column {" " "Rec" " "}
\center-column { 1 " " 2 } } } {
c'4 4 4 4 |
c'4 4 4 4 |
c'4 4 4 4 |
c'4 4 4 4 |
\break
R1*4 |
}
}
%% Recorder One
recorderOne = {
\new Staff \with {
instrumentName = \markup { Recorder 1 }
shortInstrumentName = "Rec 1" } {
R1*4 |
e'4 4 4 4 |
e'4 4 4 4 |
e'4 4 4 4 |
e'4 4 4 4 |
}
}
%% Recorder Two
recorderTwo = {
\new Staff \with {
instrumentName = \markup { Recorder 2 }
shortInstrumentName = "Rec 2" } {
R1*4 |
c'4 4 4 4 |
c'4 4 4 4 |
c'4 4 4 4 |
c'4 4 4 4 |
}
}
%% CONTENTS
contents = {
\new StaffGroup
<<
\recorderOneTwo
\recorderOne
\recorderTwo
>>
}
%% PDF
\score {
\contents
\layout {
\context {
\Staff \RemoveAllEmptyStaves
}
}
}