Thanks so much for the help again, I replace the sub input_data and sub output_data in original script with this and I get the following:

ACFX  28523  L           05/18/13  ABCCO    
ACFX  28523  L  05/01/13           ABCCO-C
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I am pasting entire script, maybe I am doing something wrong, this is a little over my head, hopefully will begin understanding better

#!/usr/bin/perl
# 
use strict;
use warnings;
use Date::Calc qw( Delta_Days );

my %hashC=();
my %hash=();
input_data(1,'out1.txt');
input_data(2,'out2.txt');
#input_data(1,'pcarry.txt');
#input_data(2,'rcarry.txt');
output_data('final.txt');


#sub input_data {
#  my ($ix,$filename) = @_;
#  open FILE1, "<", $filename or die "$filename : $!\n";
#  while ( <FILE1> ) {
#    chomp $_;
#    my ( $key, $le, $date, $company ) = split ',', $_;
#    my $pk = join "\t",$key,$le,$company;
#    push @{$hash{$pk}[$ix]},fmt_ymd($date);
#  }
#  close FILE1;
#}
sub input_data {
  my ($ix,$filename) = @_;
  open FILE1, "<", $filename or die "$filename : $!\n";
  while ( <FILE1> ) {
    chomp $_;
    my ( $key, $le, $date, $company ) = split ',', $_;    
    my $pk = join "\t",$key,$le,$company;

    # remove -C from key and store
    if ($pk =~ s/-C$//){
    #  print "-C removed $pk\n";
      $hashC{$pk} = '-C';
    }
    
    push @{$hash{$pk}[$ix]},fmt_ymd($date);
  }
  close FILE1;
}

#sub output_data {
#  my $filename = shift;
#  open OUTFILE, ">", $filename or die "$filename : $!\n";

  # primary key
#  for my $pk (sort keys %hash){
#     my ($key,$le,$company) = split "\t",$pk;

sub output_data {
  my $filename = shift;
  open OUTFILE, ">", $filename or die "$filename : $!\n";

  # primary key
  for my $pk (sort keys %hash){
    my ($key,$le,$company) = split "\t",$pk;
    # add -C back if required
    $company .= $hashC{$pk} || '';


    # get multiple dates
#    print "$pk\n";
#   my @dates  = @{$hash{$pk}[1]};
#    my @rdates = @{$hash{$pk}[2]};
    my @dates  = (defined $hash{$pk}[1]) ? @{$hash{$pk}[1]} : ();
    my @rdates = (defined $hash{$pk}[2]) ? @{$hash{$pk}[2]} : ();
    
    # even up number of dates:
    while (@dates < @rdates) {
      push @dates,'1900-01-01';
    }
    while (@rdates < @dates) {
      push @rdates,'1900-01-01';
    }
    
    # print out multiple dates for each key
    for my $date (reverse sort @dates){
    
      # use match sub if more than 1
      if (@rdates > 1){
          @rdates = match($date,@rdates);
      }
      # rdates sorted so best match is first element
      my $rdate = shift @rdates;
      print join ' ',$key,$le,fmt_mdy($date),fmt_mdy($rdate),$company,
+"\n";
    }
  }
  close OUTFILE;
}

# match dates by calc days diff
# and sorting to get least diff
sub match {
  my ($date,@rdates) = @_;
  my @days=();
  # split date into y,m,d
  my @d1 = split /\D/,$date;
  
  # calc diff and store with date
  for my $rdate (@rdates){
    my @d2 = split /\D/,$rdate;
    push @days,[$rdate,abs Delta_Days(@d1,@d2)];
  }
  
  # sort array by days
  @days = sort {$a->[1] <=> $b->[1]} @days;
  
  # extract dates 
  return map {$_->[0]} @days;
}


# change mm/dd/yy to yyyy-mm-dd
sub fmt_ymd {
  my $mdy = shift;
  $mdy =~ s/ //g;
  my ($m,$d,$y) = split /\D/,$mdy;
  if ($y < 99){ $y += 2000 };
  return sprintf "%04d-%02d-%02d",$y,$m,$d;
}

# change yyyy-mm-dd to mm/dd/yy
sub fmt_mdy {
  my $ymd = shift;
  $ymd =~ s/ //g;
  return ' 'x8 if $ymd eq '1900-01-01';
  my ($y,$m,$d) = split /\D/,$ymd;
  $y -= 2000;
  return sprintf "%02d/%02d/%02d",$m,$d, $y;
}
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