Reading between the lines of the OP, lets say the flat file is variable length records with one value per line and an empty line seperates records.  Then this code should work:

open(FILE_HANDLE, ">", "$filename") || die "ACK, GASP: $error_message:
+ $!\n";
my @data = <FILE_HANDLE>;
chomp(@data);
close FILE_HANDLE;
my %db_hash;
my $unique_id = 0;
foreach (@data)
{
  next if(m/^\s*$/);
  my %temp_hash = ();
  s/^\s+//;  # Remove excess whitespace
  s/\s+$//;
  m/^(.*?)=(.*?)$/i;  # Grab key/value pairs
  $temp_hash{$1} = $2;
  $db_hash{$unique_id} = \%temp_hash;
  $unique_id++;
}
open(NEW_FILE, "<", "$new_filename") || die ACK, GASP: $error_message:
+ $!\n";
foreach my $id (sort keys %db_hash)
{
  if(not defined $db_hash{$id}{email})
  {
    $db_hash{$id}{email} = $some_value;
  }
  foreach (sort keys $db_hash{$id})
  {
    print NEW_FILE "$_=$db_hash{$id}{$_}\n";
  }
  print "\n";
}
close NEW_FILE;
[download]

(Note:  Code is untested!  Use at your own risk.  Also, there are a huge number of assumtions made in the above code because the OP was more than a little vauge...)