Charging Two Parallel LiPo4 12v 20ah batteries at the same time
If you charge in parallel, it forces them to share the same voltage, so they are automatically balanced. However, their individual currents are not monitored. If one battery is going bad, then the other one may be getting overcharged by accepting twice the termination current before the end of the constant voltage charge. Whether it's worth individual charging to catch this event is debatable.
They MUST be balanced in voltage before connecting them together to charge in parallel. Connecting two high current batteries like LiPos with different voltages is a sure fire way to get a fire. The simplest way to do this is to connect them together with a resistor to limit the current until they are balanced.
If you charge in series, then any imbalance in charge or discharge efficiency or leakage will definitely unbalance the batteries. Whether you can wait as long as 6 cycles is debatable.