Photographing bats in flight is not only tough, but needs special equipment. The darkness and the speed with which the bats change direction will make it near impossible to use the viewfinder ;hence needs special equipments to capture them.
Recently been working on this subject with like minded friends, and able to capture some images.
A cameratrap images but with entirely different type of sensor and flash light.
There is no harm in taking flash pictures of bats flying at night, as long as it isn't in close proximity to their roost.
Canon 7D M II 11-16mm Tokina , f/8 , 1/250 , SB-25 flash at 1/32 intensity , Sensor Hahnel Captur Pro Module