for (keys  %$start) {
  my @all = ($_, keys %{$start->{$_}});

  my $processed;

  for my $setref (@$end) {
    my (@found, @not_found);

    for my $item (@all) {
      push @found, grep {$item eq $_} @$setref;
    }

    if (@found) {
      for my $item (@all) {
        push @not_found, $item unless grep {$item eq $_} @found;
      }

      push @$setref, @not_found
        if @not_found;
      $processed++;
    }
  }
  push @$end, [ @all ]
    unless $processed;
}

##</code><code>##

my $start =
  {
   a => {b => 1},
   c => {d => 2},
   d => {a => 1}
  };