"Flying blind" means you either literally or metaphorically can't see where you are going, and you aren't sure what will happen. So in this example, once they've pushed the button on the radiotherapy they aren't sure (and they can't see) if they are hitting exactly what they need to with the radiotherapy.

Hi "flying blind" here is a metaphore of flying an aeroplane whilst having your eyes covered, and implies that you don't really understand what is going to happen, but you are sure SOMETHING is going to happen; you might land or crash.