Component used: Navigation
Version used: 2.5.1 and 2.5.2
Last known working version: 2.3.5
Devices/Android versions reproduced on: Huawei P20 Light / AN 9 (EMUI 9.1.0)

So our navigation is kinda complex so I will try to simplify the configuration. If there is a nested graph with arguments which cannot be null (and no default value is supplied) and popUpTo is used to remove nested graph during destination (nested) navigation it tries to recreate nested graph as a parent for the destination being navigated to.

<navigation xmlns:android="http://schemas.android.com/apk/res/android"
    xmlns:app="http://schemas.android.com/apk/res-auto"
    android:id="@+id/parentNavGraph"
    app:startDestination="@id/parentFragment">

    <fragment
        android:id="@+id/parentFragment"
        android:label="parentFragment"
        tools:layout="@layout/fragment_parent">

        <action
            android:id="@+id/actionToChildGraph"
            app:destination="@id/childNavGraph"/>

    </fragment>

    <navigation
        android:id="@+id/childNavGraph"
        app:startDestination="@id/childFragment">

        // Note: this is a duplicate due to NavArgs since it will not see "childFragment" args
        <argument
            android:name="argumentLong"
            app:argType="long"
            app:nullable="false"/>

        <fragment
            android:id="@+id/childFragment"
            android:label="childFragment"
            tools:layout="@layout/fragment_child">

            <argument
                android:name="argumentLong"
                app:argType="long"
                app:nullable="false"/>

            <action
                android:id="@+id/actionToChildFragment2"
                app:destination="@id/childFragment2"
                app:popUpTo="@id/childNavgraph"
                app:popUpToInclusive="true"/>

        </fragment>

        <fragment
            android:id="@+id/childFragment2"
            android:label="childFragment2"
            tools:layout="@layout/fragment_child_2"/>

</navigation>

So now if the navigation is triggered like this:

findNavController().navigate(
  ChildFragmentDirections.actionToChildFragment2()
)

It will pop fragments from back stack, but it will not change parent for ChildFragment2 which will be set to childNavGraph and since it is not in the back stack anymore it will try to recreate it with default values. But argumentLong is not nullable and has no default value so it will crash:

// NOTE: this crash is from Navigation version 2.5.1
java.lang.NullPointerException: null cannot be cast to non-null type kotlin.Long
  at androidx.navigation.NavType$Companion$LongType$1.get(NavType.kt:352)
  at androidx.navigation.NavType$Companion$LongType$1.get(NavType.kt:342)
  at androidx.navigation.NavArgument.verify(NavArgument.kt:76)
  at androidx.navigation.NavDestination.addInDefaultArgs(NavDestination.kt:502)
  at androidx.navigation.NavController.addEntryToBackStack(NavController.kt:1865)
  at androidx.navigation.NavController.addEntryToBackStack$default(NavController.kt:1813)
  at androidx.navigation.NavController$navigate$4.invoke(NavController.kt:1721)
  at androidx.navigation.NavController$navigate$4.invoke(NavController.kt:1719)
  at androidx.navigation.NavController$NavControllerNavigatorState.push(NavController.kt:287)
  at androidx.navigation.fragment.FragmentNavigator.navigate(FragmentNavigator.kt:246)
  at androidx.navigation.fragment.FragmentNavigator.navigate(FragmentNavigator.kt:162)
  at androidx.navigation.NavController.navigateInternal(NavController.kt:260)
  at androidx.navigation.NavController.navigate(NavController.kt:1719)
  at androidx.navigation.NavController.navigate(NavController.kt:1545)
  at androidx.navigation.NavController.navigate(NavController.kt:1472)
  at androidx.navigation.NavController.navigate(NavController.kt:1930)

Note: Interesting thing is that it does not crash with non-nullable String argument for some reason (ah I see, it is because String NavType is nullable by default: StringType: NavType<String?> vs LongType: NavType<Long>).

Possible fixes for us:

Do not use popUpTo to pop parent (navGraph) of a Fragment (node) from XML but use popBackStack from code instead.
Add default value to argumentLong.

Basically I am not sure if this an intended behavior or a bug. Gonna mark it as a bug because it worked in 2.3.5. I understand that Destination should have a parent but what is the reason to create a parent that does not exist and will never be displayed in this case, since it was already poped and thus it should not be displayed to the user.

At the moment two solutions come to mind:

Change new Fragment (node) parent to last destination in back stack after poping. Here I am not really sure if parent is designed this way and if it can be done without breaking something else.
Make LongType and other types nullable same as StringType. Again not sure if this can be done and it probably is not a proper solution (change).

There might of course be other solutions that I cannot see.

Thank you for your time and help.