What is state of port B when port A of FT2232H is in sync. FT245 mode?
I would expect that the pins would be tristated. In order to setup sync ft245 you must first set both channels up as async ft245. Given that you are likely not planning on setting up the sync mode while a write strobe is active, the last state is tristated too. Once the resources are locked up by the sync channel, I wouldn't expect the IC to respond after that. 

Someone who has tried it may be able to confirm, but given how I expect ftdi devices to behave, I'd be surprised if that isn't the behavior you see.