Fully agree with eliminating the multiple call to keys.

I'm also a big believer in reducing nested hash references. For the small price of assigning another variable, you can eliminate the cost of several steps of hash key lookups, and improve readability as a bonus.

my $temp;
while (($entry,$temp) = each %my_hash) { 
  foreach $timeStamp ( sort keys %$temp) {

    my $hash_ref = $temp->{$timeStamp};

    my @tskeys = sort keys %$hash_ref;
    print $Hentry "$entry\t$timeStamp\t", scalar @tskeys;
    print $Hentry "\t$_\t", $hash_ref->{$_} for @tskeys;
    print $Hentry "\n";
  }
}
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