To preserve the key->{value} structure of the hash, I had to create a recursive function. This works for me:

sub merge_hashes {
    my ($x, $y) = @_;

    foreach my $k (keys %$y) {
        if (!defined($x->{$k})) {
            $x->{$k} = $y->{$k};
        } else {
            $x->{$k} = merge_hashes($x->{$k}, $y->{$k});
        }
    }
    return $x;
}
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