ThePledge
50cc
You can take 2 3S packs, for simplistic sake, 1 pack can be 11.5V, and the other can be 11.1V. Stick them on the charger as a 3S 2P pack, and the pack voltage will be 11.3V. Which is ok, but what about those cell voltages, that is what really matters. I consider anything over .05V out of balance.
The packs should both be 11.3v once they equalize so they won't be out of balance. The cells that correspond to each other in each pack will also be in balance. It isn't an average of the voltages, it's the actual voltage.
The work the charger will still have to do is bring each set of cells into balance with each other. Say cell 1 in pack A and cell 1 in pack B are together a little lower than 2a/2b and 3a/3b then the charger will need to bring those cells up to match.