$k3 = %{$hashr->{ $k1 }->{ $k2 }};
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is analogues to

$k=%hash
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$k3 is not a hashref but the scalar-value of a hash (... which produces something mostly useless like 1/8 indicating the memory use)

what you really want is either

 
$k3 = $hashr->{ $k1 }->{ $k2 };
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to get the hashref

or

 
%h3 = %{$hashr->{ $k1 }->{ $k2 }};
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to copy the nested sub-hash!