#! /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";