Building on yesterdays question, you can use the same unique identifier for an array approach.

my %names=(one   => [1,2,3],
           two   => [4,5,6],
           deux  => [4,5,6],
           three => [7,8,9]
          );
        
my %values;
for (keys %names){
        delete $names{$_} if  $values{ join ( ',', @{$names{$_}} ) }++
+;
}

for (keys  %names){
        print "$_ => ", join (", ", @{$names{$_}} ), "\n";
}
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