Surely a total loss of the APU battery even if the fire is contained within the battery box is a no go item. A large number of the emergency proceedures require the APU to start, The Hudson River incident for example would not have been successful without a working APU. I guess the main battery is slightly more important, to supply the Hot battery bus for example. but as I understand both batteries are interchangable, then the cause & fixing of this problem must be completed before the a/c can fly again