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my (%all, %clean, %fdnc);
while (my $row = $csv->getline($input)) {
...
for (sort keys %all) {
  say $_ unless $clean{$_} or $fdnc{$_};
}

my @all_nums= sort keys %all;
my @clean_nums= sort keys %clean;
...
      $dnc_nums[$i]
   ]);
}