When shutting down, how to automatically override an app prompt that interrupts the process?

I've scheduled a daily 1:00 AM shutdown of my MacBook but an app interrupts the process with a prompt that I need to manually answer before the shutdown can continue. How do I force an automatic override of this prompt or prevent it from appearing in the first place so the machine can shutdown successfully? The app in question is Audio HiJack on macOS - Sierra.