So it sounds like dump+eval does not create a true copy of the data structure.

None that I am aware of will retain knowledge that one scalar in the structure is a reference to another scalar in that same structure.

Ie. If you have this structure (which is different to what you showed, but may be what you intended):

$a = 'one'; 
$b = 'two'; 
@d = ( $a, $b, \$b );;
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Then neither Storable:

use Storable qw[ freeze thaw ];;

$x = freeze \@d;;
$y = thaw $x;;

pp $y;;
["one", "two", \"two"]

${ $y->[2] } = 'three';;

pp $y;;
["one", "two", \"three"]
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Nor Clone successfully capture that scalar reference relationship:

use Clone qw[ clone ];;

$x = clone \@d;;

pp $x;;
["one", "two", \"two"]

${ $x->[2] } = 'three';;

pp $x;;
["one", "two", \"three"]
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You could say that was a bug -- and I'd probably agree with you -- but it is a long standing one that it would appear that no one has till now seen as a problem. Which is another way of saying it is unlikely to be fixed -- or even accepted as a bug -- any time soon.