To reproduce, compile and run the example below

- expand and collapse root by clicking into the expansion icon
- expected: graphic of root must be visible always
- actual: graphic not showing

Note that the actual # of expand/collapse or which children to expand/collapse and which graphics are effected is a bit unpredictable (read: could not find a pattern).

A bit of digging revealed that the treeItem's graphic is set as the graphic of the checkBox and appears to not be removed properly. So on re-use of the cell, the checkBox still contains the old graphic which leads to removing it from its real target.

While I don't know where exactly the cleanup of the box' graphic should happen, a quick hack seems to be to null the box' graphic in updateItem, see WCheckBoxTreeCell in the example below.

public class CheckBoxTreeCellWithGraphic extends Application {

    @SuppressWarnings("unchecked")
    private Parent createContent() {
        
        TreeItem<String> root = new TreeItem<>("ROOT", new Label("really"));
        root.getChildren().add(new TreeItem<>("firstChild"));
        root.getChildren().add(new TreeItem<>("secondChild"));
        
        root.getChildren().forEach(child -> {
            child.getChildren().addAll(
                    new TreeItem<>(" of " + child.getValue(), new Label("grand1 "))
                    ,new TreeItem<>(" of " + child.getValue(), new Label("grand2"))
                    );
            child.setGraphic(new Button(child.getValue()));
        });
        
        TreeView<String> tree = new TreeView<>(root);
        // core checkBoxTreeCell
        tree.setCellFactory(CheckBoxTreeCell.forTreeView());
        // hacked checkBoxTreeCell
// tree.setCellFactory(c -> new WCheckBoxTreeCell<>());
        
        return new BorderPane(tree);
    }

    public static class WCheckBoxTreeCell<T> extends CheckBoxTreeCell<T> {
        
        CheckBox checkBoxAlias;
        public WCheckBoxTreeCell() {
            InvalidationListener checkBoxGrabber = new InvalidationListener() {
                
                @Override
                public void invalidated(Observable observable) {
                    if (checkBoxAlias == null) {
                        if (getGraphic() instanceof CheckBox) {
                            checkBoxAlias = (CheckBox) getGraphic();
                            graphicProperty().removeListener(this);
                        }
                    }
                }
                
            };
            graphicProperty().addListener(checkBoxGrabber);
        }
        
        @Override
        public void updateItem(T item, boolean empty) {
            if (checkBoxAlias != null) {
                checkBoxAlias.setGraphic(null);
            }
            super.updateItem(item, empty);
       }
 
    }

    @Override
    public void start(Stage stage) throws Exception {
        stage.setScene(new Scene(createContent()));
        stage.setTitle(FXUtils.version());
        stage.show();
    }

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

    @SuppressWarnings("unused")
    private static final Logger LOG = Logger
            .getLogger(CheckBoxTreeCellWithGraphic.class.getName());
}