Thanks! This is a little quicker, but more importantly it doesn't convert the line endings like the one-liner.

There was one bug when $buf was overwritten by the read() command. I've cleaned it up until it sorts the same number of records as the one-liner.

scalar @ARGV == 3 
   or die "usage: this.pl <suspect.txt> <good.txt> <bad.txt>\n";

open(my $fh_in, '<', shift) 
   or die("Unable to open input file: $!\n");
open(my $fh_good, '>', shift) 
   or die("Unable to open 'good' output file: $!\n");
open(my $fh_bad, '>', shift)
   or die("Unable to open 'bad' output file: $!\n");

binmode($fh_in);
binmode($fh_good);
binmode($fh_bad);

my $buf    = '';  # stores the working buffer
my $newbuf = '';  # used for reading next chunk
my $is_continued = 0; # remembers that the current record is longer th
+an it appears

local $/ = "\n";  # Because we're using binmode.
my $rec_len = 1000 + length($/);

# Working buffer size can be up to $blk_size + $rec_len bytes.
my $blk_size = 8192;

for (;;) {
   my $read = read($fh_in, $newbuf, $blk_size);

   defined $read
      or die("Unable to read input file: $!\n");
      
   $buf .= $newbuf;

   # if it didn't read anything new, flush the buffer and end
   if ($read == 0) { 
      print $fh_bad $buf if length $buf;
      last;      
   }

   while (length($buf) >= $rec_len) {
      my $pos = index($buf, $/);

      if ($pos < 0) {  # no line ending, but long enough
         print $fh_bad $buf;  
         $buf = ''; # flush, ends while
         $is_continued = 1;  
         
      } else {  # line ending found
         $pos += length($/);
         my $is_bad = $is_continued || $pos != $rec_len;
         print {$is_bad ? $fh_bad : $fh_good} (substr($buf, 0, $pos));
         substr($buf, 0, $pos, '');  # clip written section
         $is_continued = 0; # reset whenever line ending found
      }
   }
}
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