Methods of managing a lithium ion battery and of recovering branches and/or cells in the battery are provided, as well as battery management systems (BMS) and batteries implementing the methods. Branches and/or cells may be recovered by slow and deep discharging, followed by slow charging—to increase capacity, cycling lifetime and/or enhance safety thereof. BMSs may be configured to diagnose defective branches and/or cells and manage the recovery procedure with respect to changing operational loads the battery and the available internal and external charging sources.