I don't understand why you are losing data, I'm just guessing at the reason why you think you are losing data. If I'm right, then maybe you shouldn't be using a hash array, maybe you should just be using a regular array (of arrays), and then you can just sort on the element that you're currently putting in the key of the hash arrays. But since I'm not sure what you're trying to accomplish in the end, I can't be sure. Posting a small but complete example of what you're trying to do would help, instead of posting something that opens files with data that we can't see. You can post examples of reading in data using the DATA handle, e.g.:

my @lines;
while (<DATA> {
  my @array = split;
  # Don't save first two fields
  push @lines, [ @array[2..5] ];
}

# Sort 3 field from input
for my $line (sort { $a->[0] cmp $b->[0] } @lines) {
  for my $value (@$line) {
    print "$value\t";
  }
  print "\n";
}

__DATA__
a b c d e f
a b c d e f
g h i j k l
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