I don't think battery size really matters (as long as the size and charger combo doesn't result in greater than 1C charging), after all the older models have had the same charger on capacities ranging from like 6.8 to 18kW/h (and the FX/S has the same whether it's a 3.6 or 7.2, and for the latter whether it's two separate packs or one). I don't think the charger even knows or cares what the capacity is, it's just charging to a specific voltage and all the capacity changes is how long it takes to get there and how quickly it switches from constant current to constant voltage (or the other way round, always forget which it is).
Yep, if all else is the same, it simply takes twice as long to charge a battery twice the size with the same charger, which is the same added range per minute of charge in either. No need to reprogram anything.
But didn't the older FX/s use a lower battery voltage? I remember the Delta Q chargers were different for the older bikes.
-Don- Cold Springs Valley, NV