If you want for example ABCCO to match ABCCO-C then you must remove the -C from the matching key and then add it back into the report after the match. You need to ensure there are no trailing spaces in the data after the -C or modify the regex to deal with them. 
# Define a hash for pk that have -C removed
my %hashC=();
.
.
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;
    # add -C back if required
    $company .= $hashC{$pk} || '';
.
.
.

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Note : The spacing of the columns in the carry over file example is different from file 1 and 2 example. Only one space shown between column1 and 2 and no space after L. If the real data is like this you may have more problems. 
ACFX 28523, L, 05/01/13, ABCCO-C

[download]
poj

In reply to Re: issue with output of file matching by poj
in thread issue with output of file matching by rruser

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