I would keep all the floors. In such a large colony, they will use the top floors for seeds. Even if they have all the extra space, once they grow to fill it, they will clean out all the junk that they may have put in there. You could also possibly injure the queen by moving the layers so best have it set in place.
The way i design it. It will be dificult to crush the queen. If i need to add a floor. Ill doubt the queen will be far away from thw drinking floor. If she is at the top floor. A few minutes after uncovering them.she will run down to lower floors. At which point. I can place a new floor. I really like how many amts i can have in here. How easy it is to take apart. Kind of like a bee hive. I have always dream of a proper terrarium with a colomy inside. I guess ill try that with my camp. Fragilis. They are not as destructive as v. Pergandei would be inside a terrarium