Let me start by saying that I had a fully working code before deciding that I need another scene to be loaded before my main.
So, as I just mentioned instead of loading my main.fxml scene on start() I am now loading the first.fxml.
public void start(Stage primaryStage) throws Exception {
    FXMLLoader loader = new FXMLLoader(getClass().getResource("first.fxml"));
    Parent root = loader.load();
    primaryStage.setScene(new Scene(root));
    primaryStage.show();
}
and at the same time I pass the primaryStage to my main controller which is linked to both my fxml files.
Now, after the user is done with the first.fxml with the press of a button (on click handler) I load the main.fxml 
FXMLLoader loader = new FXMLLoader(getClass().getResource("main.fxml"));
Parent root = loader.load();
stage.setScene(new Scene(root));
stage.show();
which indeed loads. BUT, all of its elements (e.g. listView, button etc) are null, although there are referenced correctly in the fxml file with ids. So whenever I try to populate my listView with elements 
listView.getItems().addAll(new File("demo"));
I get a null pointer exception
Exception in thread "JavaFX Application Thread" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1774)
    at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1657)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Node.fireEvent(Node.java:8411)
    at com.sun.javafx.scene.control.behavior.TextFieldBehavior.fire(TextFieldBehavior.java:179)
    at com.sun.javafx.scene.control.behavior.TextInputControlBehavior.callAction(TextInputControlBehavior.java:178)
    at com.sun.javafx.scene.control.behavior.BehaviorBase.callActionForEvent(BehaviorBase.java:218)
    at com.sun.javafx.scene.control.behavior.TextInputControlBehavior.callActionForEvent(TextInputControlBehavior.java:127)
    at com.sun.javafx.scene.control.behavior.BehaviorBase.lambda$new$74(BehaviorBase.java:135)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Scene$KeyHandler.process(Scene.java:3964)
    at javafx.scene.Scene$KeyHandler.access$1800(Scene.java:3910)
    at javafx.scene.Scene.impl_processKeyEvent(Scene.java:2040)
    at javafx.scene.Scene$ScenePeerListener.keyEvent(Scene.java:2501)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(GlassViewEventHandler.java:197)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(GlassViewEventHandler.java:147)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleKeyEvent$354(GlassViewEventHandler.java:228)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleKeyEvent(GlassViewEventHandler.java:227)
    at com.sun.glass.ui.View.handleKeyEvent(View.java:546)
    at com.sun.glass.ui.View.notifyKey(View.java:966)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at sun.reflect.misc.Trampoline.invoke(MethodUtil.java:71)
    at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at sun.reflect.misc.MethodUtil.invoke(MethodUtil.java:275)
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1771)
    ... 46 more
Caused by: java.lang.NullPointerException
    at com.Controller.set(Controller.java:89)
    at com.Controller.populate(Controller.java:31)
    at com.Controller.handler(Controller.java:54)
    ... 56 more
Controller.class
public class Controller {
    public static Stage stage;
    public ListView listView;
    public void handler() {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("main.fxml"));
        Parent root = loader.load();
        stage.setScene(new Scene(root));
        stage.show();
        listView.getItems().addAll(new File("demo"));
    }
}
