Sample to reproduce:

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package main;

import javafx.application.Application;
import javafx.application.Platform;
import javafx.scene.Scene;
import javafx.scene.control.TextField;
import javafx.scene.layout.HBox;
import javafx.stage.Stage;

public class Main extends Application {

    public static void main(String[] args) {
        launch(Main.class, args);
    }


    @Override
    public void start(Stage stage) throws Exception {
        stage.setScene(new MainScene());
        stage.show();
    }

    class MainScene extends Scene {

        public MainScene() {
            super(new HBox(), 1024, 600);

            new Thread(new Runnable() {
                public void run() {
                    for (int i = 0; i < 2000; i++) {
                        try {
                            Thread.sleep(100);
                        } catch (InterruptedException ex) {
                        }
                        Platform.runLater(new Runnable() {
                            public void run() {
                                prepareScene();
                            }
                        });
                    }
                }
            }).start();
        }

        private void prepareScene() {
            HBox root = (HBox) getRoot();
            root.getChildren().clear();
            root.getChildren().add(new TextField());
        }
    }
}