>Question, if I use honey frames from a natural sized cell colony in the brood area, will the queen lay in it
> (and if so will it be drone brood because of larger cells?
It depends on the cell size. Some storage is drone sized.
> Or, will they tear it down, rebuild with smaller cell size and then lay in it?
Maybe, but it's doubtful. More likely they will fill it with honey if they don't want the drones.
> what about vice versa, if I'm trying to spread the brood by moving some up, once the brood has hatched, will they rebuild larger cells before they fill it with honey?
No, they will just fill it with honey if that's what they want to use it for.
>What I'm asking is, are brood frames and honey frames in a small cell colony interchangeable.
If you use 4.9mm foundation, yes. If you let them build what they want, probably not. I'd mark the frame with the measurement of the core cell size (the size in the middle) and try to keep the core of the brood nest 4.9mm or smaller.