Probably, upon removing empty lines, LilyPond could recompute the extents of the columns that bound those lines, but so far she allows space as if prefatory matter on the removed line were still present.

<< \new Staff << { c''1 \break c''2. \break c''1 } >> \new Staff \with { \RemoveEmptyStaves } << { \clef bass \key d \major d1 \break \time 3/4 R2. \key f \major \time 4/4 R1 } >> >>

slightly related to issue 448

Hmm. It looks like a bug to me that there are staves removed at all. I consider key changes as something that should stay visible even if there is no music – there is something happening on that staff.

At least I can imagine to make this configurable...

Regarding comment #1: it is configurable. That's what keepAliveInterfaces is for. I don't think it makes much sense to keep staves of silent instruments around just for key changes, though. In instrument sheets, full-bar rests will be used instead of removal. This is for partitura and summary score sheets where the timing is discernible from other staves. So will be the key signature if it is common to all instruments. And if it isn't, I don't see the point in saying "The oboe now changes its silence to the key of A major as opposed to the violin which is mute in D major."

Issue 1963 has been merged into this issue.

You’re right of course. I got confused somehow, sorry for the mess.