When storing the batteries more than a few days, DJI recommend a charge of 50%. I'm not a chemist and therefore cannot give you a reason why. I do however listen to the manufacture's suggestions when it relates to their products.
With regards to the question of how long to discharge a battery using the charger - I've only had to discharge twice to the 50% level and both times all 3 batteries placed in the DJI charger were at 100% and therefore all 3 needed to lose energy. If however 1 or 2 were at a charge below 50% I'm not sure if the power from the battery containing a greater charge is used to top up the others? Perhaps if this is the case the discharge period may be shorter.
I extremely pleased with the charger, especially the storage function, as before purchasing I used to have to turn on the Phantom to achieve a discharge. That took a long time and often I would miss the 50% point
For information I have 1 5870 mah and 2 5350 mah.