$hh{2}{6}{4} = -1;
$hh{3}{5}    = -1;
$hh{99}      = -1;
use Data::Dumper;
print Dumper( \%hh);
__END__
$VAR1 = {
          '99' => -1,
          '3' => {
                   '5' => -1
                 },
          '2' => {
                   '6' => {
                            '4' => -1
                          }
                 }
        };
[download]

No it isn't just some syntax - look at the starting hash in the OP - the problem revolves around the converting the original hash from a flattened linked list to a hash containing the equivalent linked list ... not just rewriting the hash definition..

FWIW, I've solved it thusly:

use warnings;
use strict;
use Data::Dumper;

my $fll= {
(4,-1),
(2,6),
(6,4),
(3,5),
(5,-1),
(99,-1),
};
my $ll = {};

sub doit {
    my $done = { %$fll };
    while (%$done) {
        foreach (keys %$done) {
            my ($k,$v) = ($_, $done->{$_});
            if ($v < 0) {
                %$ll = (%$ll, ($k, $v));   
                delete $done->{$k};
            } else {
                if (exists $ll->{$v}) {
                    $ll->{$k} = {$v => $ll->{$v}};
                    delete $done->{$k};
                    delete $ll->{$v};
                }
            }
        }
    }
}

doit();

print Dumper $fll,$ll;
[download]

gives:

pointo1d@pointo1d-laptop:~$ perl tst.pl
$VAR1 = {
          '6' => 4,
          '99' => -1,
          '4' => -1,
          '3' => 5,
          '2' => 6,
          '5' => -1
        };
$VAR2 = {
          '99' => -1,
          '3' => {
                   '5' => -1
                 },
          '2' => {
                   '6' => {
                            '4' => -1
                          }
                 }
        };
[download]

As, I think, required

Update:

Added my attempt at a solution.

A user level that continues to overstate my experience :-))