The new cells you have probably have some kind of built int thermal/voltage limiting system, they've come a long way. I'm not talking a full charge monitoring system like the electronics provide, just a built in safety net that helps balance a series pack.
Lipos are really only a problem when they're in a series pack, because the battery monitor circuit can't monitor each cell individually (I've never seen one in typical commercial devices at least), once a single cell is overly stressed in flight it will just get worse ultimately leading to the end of the pack, one of those cells eventually becomes a resistor. Even in the best of modern manufactoring facilities and using cells from a batch run, the chemistry ALWAYS has a lot of variation.
AG I'm guessing you're using a 3-7 cell series pack, possible in parallel?? You need better electronics in your plane, such as voltage monitoring systems that will monitor each cell and cut the whole pack off if any cell comes even close, or at least automatically lower the power level to allow the cells voltage to recover slightly, that will give you a gradual automatic power fade away that is bullet proof electrically.
The only problem is you have to monitor the specific voltage of EVERY cell in the pack simultaneously, not too hard with proper electronics knowledge, but definitely not a weekend project.
Even without any of that additional stuff set the cuttoff voltage to 3.4 volts on your current setup and you'll get at least 25% more charge/discharge cycles out of the same pack.