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So what's happening is that there are multiple NavHostFragments associated with the same R.id.nav_host_fragment FrameLayout. This is set via Navigation.setViewNavController() in the NavHostFragment's onViewCreated().

When you don't delay the setupWithNavController() call, onViewCreated() is only called on the first NavHostFragment, so everything works fine.

When you *do* delay the setupWithNavController() call, the Activity is already started, which means that onViewCreated() is called for every NavHostFragment. However, each NavHostFragment overrides the previous one. That means from the View's perspective, the NavController is the one from the navigation_notifications graph, which is why your action fails. Switching to another tab causes the newly selected tab to call setViewNavController() again, setting it back to the correct one.

There's two workarounds you can use to fix this right now (you only need one of these):

1. Manually call setViewNavController yourself using the LiveData returned by the setupWithNavController() call:
        Handler().postDelayed({
            findViewById<BottomNavigationView>(R.id.nav_view).setupWithNavController(
                graphs, supportFragmentManager, R.id.nav_host_fragment, intent).observe(this, Observer {
                Navigation.setViewNavController(findViewById(R.id.nav_host_fragment), it)
            })
        }, 1000)

2. Use the findNavController() Kotlin property extension on Fragment (which is the shorthand for the NavHostFragment.findNavController(Fragment) static method) instead of the view.findNavController() call:

// Make sure to add import androidx.navigation.fragment.findNavController

    override fun onViewCreated(view: View, savedInstanceState: Bundle?) {
        super.onViewCreated(view, savedInstanceState)
        button.setOnClickListener {
            findNavController().navigate(R.id.action_homeFragment_to_second2)
        }
    }

We'll fix the underlying issue in the library to ensure that view.findNavController() from within a Fragment works even when you have multiple NavHostFragments in the same container.

Project: platform/frameworks/support
Branch: androidx-master-dev

commit 728fbbdc3e176507580e8a09593d6564a27f13a0
Author: Ian Lake <ilake@google.com>
Date:   Wed Jun 26 15:44:08 2019

    Always setViewNavController on the root host view
   
    In cases where you have multiple NavHostFragments
    on the same container, it is important that the
    root view of each individual NavHostFragment is
    set correctly to that NavController.
   
    Test: new NavHostFragmentTest suite
    Fixes: 136021571
    Change-Id: I196c84e2bc583d6167504896f1cc068430af1088

A       navigation/navigation-fragment/src/androidTest/java/androidx/navigation/fragment/NavHostFragmentTest.kt
M       navigation/navigation-fragment/src/main/java/androidx/navigation/fragment/NavHostFragment.java

https://android-review.googlesource.com/1000392
https://goto.google.com/android-sha1/728fbbdc3e176507580e8a09593d6564a27f13a0