Refactoring a fat Controller to several other Controllers via fx:include is painful. I restored to hand-editing the FXML to cut a chunk out of the source file and replace it with fx:include. Moving things around, I bobbled a field name (txtURL versus tfURL) and had to restart the app. Then I bobbled a type "ComboBox" versus "ChoiceBox". Another restart. These are consequences of the FXML being out-of-sync with the Java code.
IntelliJ has some features for highlighting that help. For instance, the methods and fields can be related at the IDE level. However, when you're moving fast, cutting and pasting a lot, these aren't always in realtime.