Hola, le hice unos cambios a tu codigo, espero que te sirva, saludos
Código PHP:
String ultimaLinea="";
try
{
fd_in = new BufferedReader (new FileReader("origen.txt"));
fd_out = new BufferedWriter(new FileWriter(cad, true));
while ((linea = fd_in.readLine()) != null)
{
fd_out.write (linea, 0, linea.length());
fd_out.newLine();
System.out.println(linea);
ultimaLinea= linea;
}
System.out.println(ultimaLinea);
fd_in.close ();
fd_out.close ();
}