The simplest solution is to edit the FXML file and reorder the containers appropriately. As an example, my current application has a registration dialog in which a serial number can be entered. There are 5 text fields for this purpose. For the focus to pass from one text field to the other correctly, I had to list them in this way:
<TextField fx:id="tfSerial1" layoutX="180.0" layoutY="166.0" prefWidth="55.0" />
<TextField fx:id="tfSerial2" layoutX="257.0" layoutY="166.0" prefWidth="55.0" />
<TextField fx:id="tfSerial3" layoutX="335.0" layoutY="166.0" prefWidth="55.0" />
<TextField fx:id="tfSerial4" layoutX="412.0" layoutY="166.0" prefWidth="55.0" />
<TextField fx:id="tfSerial5" layoutX="488.0" layoutY="166.0" prefWidth="55.0" />
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