To potentially answer your original question, if you fire off another activity then I believe that you can save your fragment from your first activity by calling FragmentManager::putFragment(...) when onSaveInstanceState(...) is called and then getting it back later, e.g. in onCreate(...).
However, I have to agree with Mark D's response.
Incidentally I'm doing something similar in that I have a dual pane setup whereby the left pane if fixed with a number of options with each option invoking a different fragment in the right pane. Furthermore selecting an entry in the right pane can result in the right fragment being replaced by another one.
However, I have taken the approach whereby by left fragment is only responsible for displaying and handling responses from the immediate fragment which appears in the right hand pane. Furthermore each right-hand fragment is then responsible for 'replacing' itself with a new fragment and handling results sent back to it. I'm using setTargetFragment, getTargetFragment, and calling onto the target fragment's onActivityResult method to pass results back.
For me the approach I've taken is no different from when my app runs on a phone with a single pane whereby the initial option's activity only knows about the activies it fires off and subsequently these new ones fire off further activies which they know about.
It should be mentioned that my activity in my dual pane app doesn't really do much apart from loading the left pane fragment and I can't quite see the need for a single activity to ever have to manage hundreds of fragments.