Another rewrite attempt. Simplify everything you can. That makes your code easier to figure out in the future when you come back to it. Also, hashes can be nested, and I couldn't see a good reason to keep the @id array.

This may not work without some tweaking, but hopefully it will at least get you started.

#!/usr/bin/perl
use Getopt::Long;
&GetOptions('date=s'    => \$date,
            'dir=s'     => \$directory,
            'help'      => \$help);
&usage if ( defined $help || !defined $date );

my $PATH = "/Ack/$date/";
my $ftpoutbound = "/homes/ftpoutbound.db";
my %hash = ();

opendir (DIR, $PATH) || die print "can't open dir $PATH at line 62 : $
+!\n";
my @FileList = readdir(DIR);
close (DIR);
foreach $FileList(@FileList)   {
   next if $FileList =~ /^\.\.?$/;
   chomp $FileList;
   open (FILE, "$PATH$FileList") or die ("can't open $PATH$FileList :$
+!\n");
   while(<FILE>)   {
      @Fields = split /[\|\*~]/; # EDI data?
      $hash{$Fields[6]}{count}++ if ( $Fields[5] eq 'ZZ' ); # EDI?
   }
}

open (File, "$ftpoutbound") or die ("can't open $ftpoutbound at line *
+* : $!\n");
while (<File>)   {
  chomp;
  my @fields = split /\;/;
  $fields[0] =~ s/\s+//;
  $hash{$fields[0]}{transport} = $FTP_fields[7] if defined $hash{$FTP_
+fields[0]};
}
print "$_ - $hash{$_}{count} - $hash{$_}{transport}\n" for keys %hash;

sub usage { print "blah blah blah\n"; exit 1; }
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