Run the code:

    TreeTableView<Data> treeTableView;

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

    @Override
    public void start(Stage stage) throws Exception {
        treeTableView = new TreeTableView<Data>();
        treeTableView.setMaxHeight(100);
        treeTableView.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);

        treeTableView.setRoot(new TreeItem<Data>(new Data("Root")));
        for (int i = 0; i < 3; i++) {
            treeTableView.getRoot().getChildren().add(new TreeItem<Data>(new Data("item" + String.valueOf(i))));
            addItems(treeTableView.getRoot().getChildren().get(i),3);
        }
        treeTableView.getRoot().setExpanded(true);

        treeTableView.getColumns().add(new TreeTableColumn<Data, String>("Data"));
        ((TreeTableColumn<Data, String>) treeTableView.getColumns().get(0)).setCellValueFactory(new Callback<CellDataFeatures<Data, String>, ObservableValue<String>>() {
            @Override
            public ObservableValue<String> call(CellDataFeatures<Data, String> p) {
                return p.getValue().getValue().property;
            }
        });

        treeTableView.getSelectionModel().selectedIndexProperty().addListener(new ChangeListener() {
            @Override
            public void changed(ObservableValue ov, Object t, Object t1) {
                System.out.println("selectedIndexProperty : " + t1);
            }
        });

        treeTableView.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<TreeItem<Data>>() {
            @Override
            public void changed(ObservableValue<? extends TreeItem<Data>> ov, TreeItem<Data> t, TreeItem<Data> t1) {
                System.out.println("selectedItemProperty : " + t1);
            }
        });

        treeTableView.getSelectionModel().getSelectedItems().addListener(new ListChangeListener<TreeItem<Data>>() {
            @Override
            public void onChanged(Change<? extends TreeItem<Data>> change) {
                System.out.println("SelectedItems : " + treeTableView.getSelectionModel().getSelectedItems());
            }
        });

        treeTableView.getFocusModel().focusedIndexProperty().addListener(new ChangeListener<Number>() {
            @Override
            public void changed(ObservableValue<? extends Number> ov, Number t, Number t1) {
                System.out.println("focusedIndexProperty : " + t1);
            }
        });

        treeTableView.getFocusModel().focusedItemProperty().addListener(new ChangeListener<TreeItem<Data>>() {
            @Override
            public void changed(ObservableValue<? extends TreeItem<Data>> ov, TreeItem<Data> t, TreeItem<Data> t1) {
                System.out.println("focusedItemProperty : " + t1);
            }
        });

        VBox vb = new VBox();
        vb.getChildren().addAll(treeTableView);

        Scene scene = new Scene(vb, 300, 300);
        stage.setScene(scene);
        stage.show();
    }

    private void addItems(TreeItem<Data> item, int amount) {
        for (int i = 0; i < amount; i++) {
            item.getChildren().add(new TreeItem<Data>(new Data(item.getValue().property.get() + "-" + String.valueOf(i))));
        }
    }

    class Data {

        public StringProperty property;

        public Data(String data) {
            property = new SimpleStringProperty(data);
        }

        @Override
        public String toString() {
            return property.get();
        }
    }

expand all items.
select some item.
press ctrl+a.

collapse some item in the middle (item 1 for instance). focus and selected item will be moved to that position. I expect them to stay, where they were before collapsing.

Sample output:
SelectedItems : [TreeItem [ value: item0-1 ]]
selectedItemProperty : TreeItem [ value: item0-1 ]
selectedIndexProperty : 3
focusedItemProperty : TreeItem [ value: item0-1 ]
focusedIndexProperty : 3
SelectedItems : []
SelectedItems : [TreeItem [ value: item0-1 ]]
SelectedItems : []
SelectedItems : [TreeItem [ value: Root ], TreeItem [ value: item0 ], TreeItem [ value: item0-0 ], TreeItem [ value: item0-1 ], TreeItem [ value: item0-2 ], TreeItem [ value: item1 ], TreeItem [ value: item1-0 ], TreeItem [ value: item1-1 ], TreeItem [ value: item1-2 ], TreeItem [ value: item2 ], TreeItem [ value: item2-0 ], TreeItem [ value: item2-1 ], TreeItem [ value: item2-2 ]]
selectedItemProperty : TreeItem [ value: item2-2 ]
selectedIndexProperty : 12
focusedItemProperty : TreeItem [ value: item2-2 ]
focusedIndexProperty : 12
selectedItemProperty : TreeItem [ value: item1 ] // here I collapsed the item.
selectedIndexProperty : 5
focusedItemProperty : TreeItem [ value: item1 ]
focusedIndexProperty : 5

BTW, selected items array was not updated.

Affected tests:
ControlsAutomatedTestSuite/javafx/scene/control/test/treetable/TreeTableAsTreeTest/selectionCorrectnessOnCollapsingCtrlATest