This should work also -- the "$$href" part means that you are dereferencing $href and looking to identify a scalar value somewhere in the referenced structure; this way, you get to avoid using "->" altogether:

while(($key, $value) = each(%$href)) {
   $$href{$key}[1][0][0] = 1;
   ...
   print "$key/1/0/0 = $$href{$key}[1][0][0]\n";
}
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Note that if you wanted to refer to an entire array that is referenced in the structure, you need to use extra curly brackets around the expression that follows the @ sigil:

   my @toparray = @{$$href{$key}};
   my @midarray = @{$$href{$key}[1]};
   my @endarray = @{$$href{$key}[1][0]};
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