I have a pond filter but my mum and dad keep turning the pump supplying the water to it will this will kill the beneficial bacteria, it is left off for nearly a whole day.

Pond filter should be disabled only during the cleaning time. Turning off just a few days won't kill bacteria, but that it will continue to grow, too. Your parents are probably shutdown the pump to save electricity, but that's not good for the pond. There are many other ways to save electricity, which could make up for all the uses pump.