I had an internship at a company that made lithium battery packs. The control boards on the packs have primary cell protection provided by a specialized micro controller that monitors cell voltages and prevents over/under charge levels and monitors current, however they also have secondary protection ICs that are hardware based that will shut down the pack should the cells reach dangerously high levels, as well as fuses to prevent dangerous levels of current.

Net result, changing battery firmware can reduce usefulness of battery (higher charging degrades cell life, blow fuses etc) but the packs should have hardware based protection from being a safety hazard