You could just limit the voltage on each cell with a bypass device that conducts above the maximum voltage for each cell.
It is also a good idea to reduce the charge rate to C/10 or so if any cell has a very low voltage, but really the discharge should have been stopped before that point.
When I needed to have three LiIon cells in series, I used a relay to disconnect them for charging. Each cell has a separate charger, and they all share a common negative when charging.