Not sure if I understood your problem correctly, but here's the solution to what I understood:

@RE_QUERY = sort {
   for my $i (3, 2) {
      return $QUERY{$a}[$i] cmp $QUERY{$b}[$i] 
            if defined $QUERY{$a}[$i] && 
               defined $QUERY{$b}[$i] && 
               $QUERY{$a}[$i] cmp $QUERY{$b}[$i];
   }
   return $QUERY{$a}[0] cmp $QUERY{$b}[0];
} keys % QUERY;
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