Run the given code below. You will find that the 2nd item in TreeView does not receive focus, despite calling:

treeView.getFocusModel().focus(1);

This only happens when you change a scene (but not replace it completely). Work-arounds to make this work as expected:

1) Replace the entire scene...
2) Wrap the focus(1) call in Platform.runLater() -- despite already being on the JavaFX thread.

I would expect neither of the work-arounds to be required to get this to work directly.

public class TreeItemFocusTest extends Application {
 
  public static void main(String[] args) {
    Application.launch(args);
  }
 
  @Override
  public void start(Stage primaryStage) throws Exception {
    VBox vbox = new VBox();
 
    BorderPane borderPane = new BorderPane();
    Button button = new Button("Sometihng to grab focus");
 
    final TreeView<String> treeView = new TreeView<String>();
 
    TreeItem<String> root = new TreeItem<String>("Root");
 
    root.setExpanded(true);
 
    treeView.setRoot(root);
 
    root.getChildren().add(new TreeItem<String>("Item 1"));
    root.getChildren().add(new TreeItem<String>("Item 2"));
    root.getChildren().add(new TreeItem<String>("Item 3"));
    root.getChildren().add(new TreeItem<String>("Item 4"));
 
    vbox.getChildren().addAll(button, treeView);
 
    Scene scene = new Scene(borderPane);
 
    primaryStage.setScene(scene);
    primaryStage.show();
 
    // Change the borderpane contents here
    borderPane.setCenter(vbox);
 
    // Give desired item the focus
    treeView.requestFocus();
    treeView.getFocusModel().focus(1);
  }
}