You are running into a problem because you are instantiating and keeping references to your fragments outside of PagerAdapter.getItem, and are trying to use those references independently of the ViewPager. As Seraph says, you do have guarantees that a fragment has been instantiated/added in a ViewPager at a particular time – this should be considered an implementation detail. A ViewPager does lazy loading of its pages; by default it only loads the current page, and the one to the left and right.
If you put your app into the background, the fragments that have been added to the fragment manager are saved automatically. Even if your app is killed, this information is restored when you relaunch your app.
Now consider that you have viewed a few pages, Fragments A, B and C. You know that these have been added to the fragment manager. Because you are using FragmentPagerAdapter and not FragmentStatePagerAdapter, these fragments will still be added (but potentially detached) when you scroll to other pages.
Consider that you then background your application, and then it gets killed. When you come back, Android will remember that you used to have Fragments A, B and C in the fragment manager and so it recreates them for you and then adds them. However, the ones that are added to the fragment manager now are NOT the ones you have in your fragments list in your Activity.
The FragmentPagerAdapter will not try to call getPosition if there is already a fragment added for that particular page position. In fact, since the fragment recreated by Android will never be removed, you have no hope of replacing it with a call to getPosition. Getting a handle on it is also pretty difficult to obtain a reference to it because it was added with a tag that is unknown to you. This is by design; you are discouraged from messing with the fragments that the view pager is managing. You should be performing all your actions within a fragment, communicating with the activity, and requesting to switch to a particular page, if necessary.
Now, back to your problem with the missing activity. Calling pagerAdapter.getItem(1)).update(id, name) after all of this has happened returns you the fragment in your list, which has yet to be added to the fragment manager, and so it will not have an Activity reference. I would that suggest your update method should modify some shared data structure (possibly managed by the activity), and then when you move to a particular page it can draw itself based on this updated data.