Yes. But discharged to what level? Since the battery (main) is part of a critical backup system (brakes), there is a requirement to maintain it to some minimum level of charge. Because there are parasitic loads and some level of self discharge, the charge cycle will periodically have to be started. How this is sensed and how this level relates to the charging algorithm could affect the health of the battery.
LiON batteries do not like to be 'float charged' due to the voltage inflection phenomenon (higher state of charge at a given temp results in a lower terminal voltage) and resulting runaway. So it would be expected that the battery/charger system will cycle between full (charger turns off) and some recharge threshold point charger turns back on).