#! /usr/bin/perl
use strict;
use warnings;

use List::Util qw( first );

my $fileA         = "A.txt";
my $fileB         = "B.txt";
my $outfile       = "C.txt";
my $criteria_size = 20;


# be sure you have enough memory for this!
my @reference = do { open my $fh, '<', $fileB; <$fh> };

open my $fhout, '>', $outfile   or die "open($outfile,w) failed: $!\n";
open my $fhin, '<', $fileA      or die "open($fileA,ro) failed: $!\n";

while ( my $lineA = <$fhin> ) {

    my $critA = substr( $lineA, 0, $criteria_size );

    # return first line with matching reference number and leave it in @reference
    my $lineB = first { substr( $_, 0, $criteria_size ) == $critA } @reference;
    print $fhout ( $lineB ? $lineB : $lineA );
}

close $fhin;
close $fhout                    or die "close($outfile) failed: $!\n";

#! /usr/bin/perl
use strict;
use warnings;

use List::Util qw( first );

my $fileA         = "A.txt";
my $fileB         = "B.txt";
my $outfile       = "C.txt";
my $criteria_siue = 20;

# be sure you have enough memory for this!
my %reference;

open my $fh, '<', $fileB    or die "open($fileB,ro) failed: $!\n";
# expensive in memory usage (as it uses temporary lists in memory)
# %reference = map { substr( $_, 0, $criteria_size ) => $_  } <$fh>;

while ( my $line = <$fh> ) {
    $refernce{ substr( $line, 0, $criteria_size ) } = $line;
}
close $fh;

open my $fhout, '>', $outfile   or die "open($outfile,w) failed: $!\n";
open my $fhin, '<', $fileA      or die "open($fileA,ro) failed: $!\n";

while ( my $lineA = <$fhin> ) {

    my $critA = substr( $lineA, 0, $criteria_size);

    print $fhout ( exists $reference{$critA} ? $reference{$critA} : $lineA );
}

close $fhin;
close $fhout                    or die "close($outfile) failed: $!\n";

# Variante 1
real    0m0.286s
user    0m0.284s
sys     0m0.001s

# Variante 2
real    0m0.018s
user    0m0.011s
sys     0m0.005s