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binmode $fh_in;
binmode $fh_out;
...
while (<$fh_in>) {
   print $fh_out "$_\x0D\x0A";
}

binmode $fh_out;

...
   my $rec = substr($str, 0, 90, '');
   print $fh_out "$rec\x0D\x0A";
}