To reproduce, run example below: it creates a bunch of checkBoxTreeItems with one selected. Note that parent state is indeterminate as expected. Press button to remove the selected treeItem.

- expected: parent state changed to unselected
- actual: parent state still indeterminate

public class CheckBoxTreeCellOnRemove extends Application {

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

    @Override
    public void start(Stage stage) throws Exception {
        stage.setTitle(VersionInfo.getRuntimeVersion());
        stage.setScene(getScene());
        stage.show();
    }

    private Scene getScene() {
        
        List<TreeItem<String>> ls = new ArrayList<TreeItem<String>>(10);
        for (int i = 0; i < 10; i++) {
            ls.add(new CheckBoxTreeItem<String>("Test " + i));
        }
        
        TreeView<String> tv = new TreeView<String>();
        tv.setRoot(new CheckBoxTreeItem<String>("Root"));
        
        tv.getRoot().getChildren().addAll(ls);
        tv.getRoot().setExpanded(true);
        
        tv.setCellFactory(CheckBoxTreeCell.forTreeView());
        BorderPane root = new BorderPane();
        root.setCenter(tv);
        
        Button removeSelected = new Button("removeSelected");
        removeSelected.setOnAction(e -> {
            TreeItem item = tv.getSelectionModel().getSelectedItem();
            if (item == null || item == tv.getRoot()) return;
            tv.getRoot().getChildren().remove(item);
        });
        HBox buttonPane = new HBox(removeSelected);
        root.setBottom(buttonPane);
        
        return new Scene(root, 600, 400);
    }
 
}