That deleted scene is not canon. It was completely taken out because it would not have made sense. If Burke were to be there at all, he would at the most only have a Face Hugger on him. If Burke WAS taken to the AP though, he is dead. Everything in the AP is definitely destroyed. If the idea that there is another Hive or area outside the AP where hosts (Hudson?) was being taken to then that is where we will find out.