As far as I can tell, they have now got enough B series railcars to do the whole Mandurah/ Butler line with all services being run as 6 car sets during the peaks (except during special events), and then some spare cars left over.
i think you'll find, to increase capacity on the heritage lines, services that were once run as 2 cars are now running as either 3 cars (with a B series) or 4 cars (using the now free railcars form the services taken over by B series).
This situation may change when FAL comes online.
As far as I'm aware all the original A series railcars are still in service. There will always be one or two sets undergoing maintenance/ overhaul, so they'll be off traffic, but none as far as I'm aware have been withdrawn from service.