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

#!/usr/bin/env perl

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

dd $VAR1;

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