Assuming you can match the records using the number in col 3 then read the values from the previous month into a hash

open PREV,'<','prev.txt' or die "$!";
my %prev_days=();
#BIGCO-C  CMO 180304 L 6/30/13  2
while (<PREV>){
  chomp;
  my @f = split /\s+/,$_;
  $prev_days{$f[2]} = $f[5];
}
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and then add them into your $amt calc

while (<$file>) {
  my @f = split '\s+', $_;
  $cnt++;
# fill empty dates with month end
  my @ymd1 = split ',',$f[4] //= $prev_mth_end;
  my @ymd2 = split ',',$f[5] //= $prev_mth_end;
  my $diff = Delta_Days(@ymd1, @ymd2);
  my $prev = $prev_days{$f[2]} //= 0;

  my $amt = ($diff + $prev > 3) ? $diff + $prev - 3 : 0;
  my $cost = ($amt * 100);
  my $pfmt = "%-14s %-5s %-8s %-3s %-12s %-12s %-6s %-6s %-6s %-6s\n";
  printf OUT $pfmt, @f[0..3], fmt_mdy($f[4]), fmt_mdy($f[5]), $diff, $
+amt, fmt_curr($cost), $prev;
}
[download]

poj