Think if you wrote your two measures this way, it works:
\score {
\context PianoStaff <<
\context Staff = upper {
\set Staff.extraNatural = ##f
\time 2/2 \clef treble \key bf \major
<< {cs''8 c'' cs'' e'8~ e'4. cs''8 b' as' b' cs'~ cs'2} \\
{cs'1 s1} >>
}
\context Staff = lower {
\set Staff.extraNatural = ##f
\time 2/2 \clef bass \key bf \major
<< {a2 b4 a fs2 | fs4 es} \\
{e1 | <<gs cs>>} >>
} >>
}
The g# that you had in the upper voice shifted to the bass clef was
throwing off the spacer. If you just make a chord with the c#,
there's no need to shift voices around.
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