don't switch while the engines are running unless you are sure that the wiring is so that the alternator is always connected to some battery bank.
This is one of the reasons you cannot use your alternator connected to a LifePo4 (Lithium) battery since the BMS will disconnect abruptly when fully charged or some some other abnormal parameter may occur which will also cause a disconnect. In other words, same as removing the battery from a running alternator. Poof goes the alternator.