First, if ( $line =~ /^SY/ ) { s/^SY/CN/ } is redundant. And if you need to keep track of what the "next" line is, set a flag:

my $is_sy;
for my $line (@lines) {
  if ( $is_sy ) {
    $line =~ s/^SY/  /;
    $is_sy = 0;
  } else {
    $is_sy = ( $line =~ s/^SY/CN/ );
  }
}
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