A few alternatives after re-reading what you are doing. It seems that there are two separate issues, weight and charging.
A simple solution to charging is to use the packs as you are and then remove them from the plane for charging. Once removed, use the mentioned balance plug Y harness for charging, and charge them as one with both the power and balance harnesses. The balance harness can be removed for flying. Mark pack 1 and pack 2 so that the power Y and balance Y join the packs the same.
Or create hardwiring of those harnesses using the harnesses as "templates," for some weight savings.
Or hard wire the power Y and use the balance y for charging only which saves weight.
Another easy solution for charging is to remove the power Y connection, back to two 3 cell packs and use a parallel board to charge and balance the packs at the same time. Technically simple, but same weight as now.
The lightest is to totally rewire at the solder end and make a 6 cell pack as above. Technically a bit more difficult, but saves weight and fiddling each time, once done.
Or wait for better ideas as others enter the discussion, which could be the best idea :)