Questo è il codice della copia un pò modificato per il salvataggio, ti scrivo anche quello funzionante per la copia?
codice:
//funzione salva file   
    public static void saveFile() {
        JFileChooser chooser = new JFileChooser();
        File modello = new File("modello_programma.rtf");

        chooser.setFileFilter(new javax.swing.filechooser.FileFilter() {
          public boolean accept(File f) {
            return f.getName().toLowerCase().endsWith(".rtf")
                || f.isDirectory();
          }

          public String getDescription() {
            return "Documento *.RTF";
          }
        });

        int s = chooser.showSaveDialog(new JFrame());
         if (s == JFileChooser.APPROVE_OPTION) {
          try {
			save(modello);
		} catch (IOException e) {
			System.err.println(e.getMessage());
		}
          System.out.println(modello);     
          
        }
      }
    
    //salvataggio a livello fisico
    public static void save(File modello)
    throws IOException {
    File fromFile = modello;
    File toFile = new File("modello_programma.rtf");

    if (toFile.isDirectory())
      toFile = new File(toFile, fromFile.getName());

    if (toFile.exists()) {
     if (!toFile.canWrite())
      throw new IOException("FileCopy: "
          + "destination file is unwriteable: " + modello);
      System.out.print("Overwrite existing file " + toFile.getName()
          + "? (Y/N): ");
      System.out.flush();
      BufferedReader in = new BufferedReader(new InputStreamReader(
        System.in));
      String response = in.readLine();
    if (!response.equals("Y") && !response.equals("y"))
      throw new IOException("FileCopy: "
          + "existing file was not overwritten.");
    } else {
      String parent = toFile.getParent();
       if (parent == null)
        parent = System.getProperty("user.dir");
        File dir = new File(parent);
    if (!dir.exists())
      throw new IOException("FileCopy: "
          + "destination directory doesn't exist: " + parent);
    if (dir.isFile())
      throw new IOException("FileCopy: "
          + "destination is not a directory: " + parent);
    if (!dir.canWrite())
      throw new IOException("FileCopy: "
          + "destination directory is unwriteable: " + parent);
  }

  FileInputStream from = null;
  FileOutputStream to = null;
  try {
    from = new FileInputStream(fromFile);
    to = new FileOutputStream(toFile);
    byte[] buffer = new byte[4096];
    int bytesRead;

    while ((bytesRead = from.read(buffer)) != -1)
      to.write(buffer, 0, bytesRead); // write
  } finally {
    if (from != null)
      try {
        from.close();
      } catch (IOException e) {
        ;
      }
    if (to != null)
      try {
        to.close();
      } catch (IOException e) {
        ;
      }
  }
}