If you keep the number of charges the same they should be fine.
I always set the lvc for 3.2v per cell when I run a pair of packs in series. One pack may be "stronger" than the other, and the higher lvc setting helps the weaker pack...
I do the same if I run a pair of packs in parallel too, for the same reason...
if you are balancing them together as 1 battery, and they both have the same number of charges, but one hasn't been drained as long as the other, it will still work, but it will take a while for the balancer to get the batteries together, but if your balancer can't communicate with the charger (is not built in or does not have a data port) then it may not be able to get them together.
As i said before i've a hyperion 0610 DUO charger with integrated balancer. Please tell me what's for you "balance them as a single pack"?????
IF i run them separatly but i charge/balance them in same time on my charger (one on each chanel) is it the same thing than charging them as a single pack???????