open(my $fh_in, '<', ...)
   or die("Unable to open input file: $!\n");

open(my $fh_good, '>', ...)
   or die("Unable to open 'good' output file: $!\n");

open(my $fh_bad, '>', ...)
   or die("Unable to open 'bad' output file: $!\n");

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

my $buf  = '';
my $skip = 0;

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

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

for (;;) {
   my $read = read($fh_in, $buf, $blk_size, length($ofs));

   defined $read
      or die("Unable to read input file: $!\n")

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

      if ($pos < 0) {
         print $fh_bad $buf;
         $buf = '';
         $skip = 1;
      } else {
         $pos += $ofs + length($/);
         my $bad = $skip || $pos != $rec_len;
         print { $bad ? $fh_bad : $fh_good } (substr($buf, 0, $pos));
         substr($buf, 0, $pos, '');
         $skip = 0;
      }
   }

   if ($read == 0) {
      print $fh_bad $buf if length $buf;
      last;      
   }
}

[download]

Untested.

Update: Cleanup.

In reply to Re: Thrashing on very large lines by ikegami
in thread Thrashing on very large lines by chr1so

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