On my A6500, you can deploy, but not retract. The little lever just presses the pop up button. Unless the A6400 has some sort of power retraction, my guess is that it's a one way operation. Convenient, as it's easy to forget to pop up the flash before sealing the housing.
Turning off the flash isn't hard. Getting to the menu option should be accessible from the FN menu. However, if I just need to take a few ambient light shots, I just turn off the strobes and don't worry that the internal flash is firing.