One way is to loop over the indices of the array rather than the array items.

for( my $i = 0; $i <= $#lines; $i++ ) {
    if ( $lines[$i] =~ s/^SY(?= )/CN/ ) {
        if ( defined $lines[$i+1] ) {
            $lines[$i+1] =~ s/^SY(?= )/  /;
        }
     }
}
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Another way is to join all the lines into one large string and do replacements.

Still another way would be to use a flag variable to say when the previous line matched.

my $previous_line_matched = 0;
foreach my $line ( @lines ) {
    if ( $previous_line_matched ) {
        $line =~ s/^SY(?= )/  /;
    }
    if ( $line =~ s/^SY(?= )/CN/ ) {
        $previous_line_matched = 1;
        next;
    }
    $previous_line_matched = 0;
}
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