The presented paper discusses the most often damages applying for lithium traction and non-traction cells. The focus is therefore given on investigation of possibilities related to the recovery of such damaged lithium-ion batteries, more specifically after long-term short-circuit and deep discharge. For this purpose, initially, the short-circuit was applied to the selected type of traction LiFePO4 cell. Also, the deeply discharged cell was identified and observed. Both damaged cells would exhibit visible damage if electro-mechanical properties were measured. Individual types of damage require a different approach for battery regeneration to recover cells as much as possible. For this purpose, experimental set-up for automated system integrating proposed recovery methods were realized, while battery under test undergone a full-range of regeneration procedure. As a verification of the proposed regeneration algorithms, the test of delivered Ampere-hours (Ah) for various discharging currents was realized both for short-circuited as well as deeply discharged cells. Received results have been compared to the new/referenced cell, which undergoes the same test of delivered Ah. From the final evaluation is seen, that proposed procedure can recover damaged cell up to 80% of its full capacity if short-circuit was applied, or 70% if a deeply discharged cell is considered.