I am just a gamer that loves anything and everything sci-fi from Halo, to Homeworld, to Warhammer 40k, to Starwars, Starcraft, Sins of a Solar Empire and Dead Space my new personal favorite.
This is just an idea that came to mind while I was bored out of my mind.
I guess that would only happen in an alternative universe.
You could try to have the whole oiginal ship infected with the former lower decks still connected.
But with the additional resource drop off removed.