He creado una aplicación usando jfxPanel dentro del componente swing. El problema al que me enfrento es que no puedo cambiar los archivos fxml. Cuando se hace clic en un botón del fxml, quiero deshacerme de ese fxml y cargar otro archivo fxml allí. Esto es lo que he hecho hasta ahora.

public class NonResponsiveButtons extends JFrame {
    NonResponsiveButtons nrb;
    BottomPanelIncomingController bpic;
    JPanel panel; 
    JPanel bPanel;

    private int applicationWidth_600 = 600;
    private int applicationHeight_600 = 600;

    private int upperPanelHeight_535 = 535;
    private int bottomPanelHeight_65 = (applicationHeight_600-upperPanelHeight_535); 


    public static void main(String[] args) {
    new NonResponsiveButtons();
    }



    public NonResponsiveButtons(){
        final JFXPanel fxPanel = new JFXPanel();

        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
            // TODO Auto-generated method stub
                try{
                    new JFXPanel();
                    add(getJPanel(), BorderLayout.CENTER);
                    add(getJBottomPanel(), BorderLayout.PAGE_END);
                    bPanel.add(fxPanel, BorderLayout.CENTER);

                    Platform.runLater((new Runnable() {

                    @Override
                    public void run() {
                        // TODO Auto-generated method stub
                        initFX(fxPanel);    
                    }
                })) ;

            }
                catch(Exception e){
                    System.out.println("Error in swing utilities thread :" + e.getMessage());
            }

        }
    });

    this.setSize(applicationWidth_600, applicationHeight_600);
    setLocationRelativeTo(null);
    BorderLayout borderLayout = new BorderLayout();
    setLayout(borderLayout);

    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);     
    setVisible(true);
}


private void initFX(JFXPanel jfxPanel) {
    try {
        FXMLLoader fxmlLoader = new FXMLLoader(getClass().getResource("fxmlDesign.fxml"));
        Parent root = (Parent) fxmlLoader.load();
        Scene scene = new Scene(root, 600, 65);
        jfxPanel.setScene(scene);

        fxmlLoader.getController();
        bpic = new BottomPanelIncomingController();
        bpic.setNonResoinsiveButtons(this);

    } catch (IOException exc) {
        exc.printStackTrace();
        System.exit(1);
    }
}

public void loadSecondFxml(){
    System.out.println("loading second fxml");
}   

private JPanel getJPanel(){
    if(panel == null){
    panel = new JPanel();
    panel.setSize(applicationWidth_600,upperPanelHeight_535);
    panel.setBackground(Color.gray);
    }
    return panel;
}

private JPanel getJBottomPanel(){
    if(bPanel == null){
        bPanel = new JPanel();
        bPanel.setSize(applicationWidth_600, bottomPanelHeight_65);
        bPanel.setBackground(new Color(8, 16, 19));
    }
    return bPanel;
}   

}

La clase BottomPanelIncommingController. El controlador fxml

public class BottomPanelIncomingController implements Initializable {
 NonResponsiveButtons nrb;

    @Override
    public void initialize(URL arg0, ResourceBundle arg1) {
    // TODO Auto-generated method stub
    System.out.println("HEllo");
    }

    public void setNonResoinsiveButtons(NonResponsiveButtons nrb){
    this.nrb = nrb;
    }

    @FXML
    public void callAccepted(ActionEvent event){
    System.out.println("From controller");
    nrb.loadSecondFxml();
    }
 }