Some questions about your solution and data. Some data from file2:

WILYCO    CNW   437106 L 2013,07,08
WILYCO    MKT     4399 L 2013,07,03
WILYCO    MKT     4559 L 2013,07,23 2013,07,26
[download]

What do you want to do when there is not a second date? Also, is it possible to not have a first date? What would you do in that case? Because, your code is (date calculations flawed I think - see next question about the dates):

my @ymd1 = split ',',$dates[4] //= $prev_mth_end;
my @ymd2 = split ',',$dates[5] //= $prev_mth_end;
[download]

Do you really want to assign $prev_mth_end to both if both are blank?

# work out end of current month
my ($y,$m,$d) = Today();
my $mth_end = sprintf "%04d,%02d,%02d",$y,$m,Days_in_Month($y,$m);
# ($year,$month,$day) = Add_Delta_Days($year,$month,$day,$Dd);
my $prev_mth_end = sprintf "%04d,%02d,%02d",
                   Add_Delta_Days($y,$m,1,-1);
[download]

It is August now and your date code is using Today(), but your file 2 data is all for the month of July. I think this might be a problem, as the dates won't pertain to July but instead August.

I don't see where you are taking into account for the days from the previous month (June, file 1).

For example, a record from file 1 shows 2 days:

BIGCO-C  MKT   575 L 6/30/13  2

The corresponding record from file 2 shows:

BIGCO-C   MKT      575 L 2013,07,01 2013,07,02

Subtracting 2013,07,01 from 2013,07,02 = 1 day? Then, total days be 2 + 1 = 3 in this case?

From that, subtracting the 3 free days would give 0 billing days? Are you calculating Demurrage?