$_->[2] eq $barcode_pair_35 and ++$_->[3] for values %$VAR1;

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dump;

my $VAR1 = {
    '1' => [ 'AGCTCGTTGTTCGATCCA', 'GAGAGATAGATGATAGTG', 'TTTT_CCCC', 0 ],
    '2' => [ 'AGCTCGTTGTTCGATCCA', 'GAGAGATAGATGATAGTG', 'TTTT_AAAA', 0 ]
};

dd $VAR1;

my $barcode_pair_35 = 'TTTT_CCCC';

$_->[2] eq $barcode_pair_35 and ++$_->[3] for values %$VAR1;

dd $VAR1;

##</code><code>##

{
  1 => ["AGCTCGTTGTTCGATCCA", "GAGAGATAGATGATAGTG", "TTTT_CCCC", 0],
  2 => ["AGCTCGTTGTTCGATCCA", "GAGAGATAGATGATAGTG", "TTTT_AAAA", 0],
}
{
  1 => ["AGCTCGTTGTTCGATCCA", "GAGAGATAGATGATAGTG", "TTTT_CCCC", 1],
  2 => ["AGCTCGTTGTTCGATCCA", "GAGAGATAGATGATAGTG", "TTTT_AAAA", 0],
}