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my %seen_values;
for my $aref (@array_of_arrayrefs) {
  $aref = [ map { $seen_values{$_}++ ? () : $_ } @$aref ];
}

my %seen_values;
my @new_AofA = map { $seen_values{$_->[0]}{$_->[1]}++ ? () : $_ } @Aof
+A;