Another question. If you remove the 50% charged batteries from the charger and place them in a case, will they start discharging after the time set in the RC?Yes.
The charged count increments by one each time the battery is charged from 0% to 100%. That means the counter will never increment until you've charged the battery at least twice (since you're never charging it from 0% to 100% in a single charge). So, if you charge the battery from 50% to 100% twice in a row, the count will increment by one.