I was always pretty sure that the running engine couldn't have damaged your charger. Good to hear that the real problem was one that could easily be fixed.
Regarding the overcharged LiPo's: There is even less possibility that a running engine could cause the charger to over-charge a LiPo. The charge termination voltage has nothing to do with the input voltage of the charger. Most likely the problem was the charger being set incorrectly for the battery it was charging.