This bug can be reproduced using attached application as following:
1. select 'item1' -> listener on selected items is called
2. press 'r' (it removes all children) -> listener is not called.
3. press 'g' (gets the current selection) -> current selection is correct, 'root' in this case.

Expected behavior -> listener in p. 2 is called.

import javafx.application.Application;
import javafx.collections.ListChangeListener;
import javafx.scene.Scene;
import javafx.scene.control.MultipleSelectionModel;
import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeView;
import javafx.scene.input.KeyCode;
import javafx.scene.input.KeyCodeCombination;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class Main extends Application {

    private final TreeItem<String> item = new TreeItem<>("child1");

    @Override
    public void start(final Stage primaryStage) throws Exception {
        final VBox box = new VBox();
        final Scene scene = new Scene(box);
        primaryStage.setScene(scene);
        final TreeView<String> treeView = getTreeView();
        box.getChildren().add(treeView);
        primaryStage.show();

        scene.getAccelerators().put(new KeyCodeCombination(KeyCode.R), () -> {
            treeView.getRoot().getChildren().removeIf(item -> true);
        });
        scene.getAccelerators().put(new KeyCodeCombination(KeyCode.A), () -> {
            treeView.getRoot().getChildren().add(item);
        });
        scene.getAccelerators().put(new KeyCodeCombination(KeyCode.G), () -> {
            final MultipleSelectionModel<TreeItem<String>> selectionModel = treeView.getSelectionModel();
            System.out.println(selectionModel.getSelectedItems());
        });
    }

    private TreeView<String> getTreeView() {
        final TreeItem<String> root = new TreeItem<>("root");
        root.getChildren().add(item);

        final TreeView<String> treeView = new TreeView<String>(root);
        root.setExpanded(true);
        treeView.getSelectionModel().select(root);
        treeView.getSelectionModel().getSelectedItems().addListener((final Change<? extends TreeItem<String>> c) -> {
            System.out.println(treeView.getSelectionModel().getSelectedItems());
        });
        return treeView;
    }

    public static void main(final String[] args) {
        launch(args);
    }
}