If a flashlight is aimed directly at your camera at night, this will create high contrast in the scene between the flashlight and its flare, and the subject which is in the dark.
You can fix that by reducing the intensity of the light, but you can also fix it from the other end, by increasing the amount of light on the subject. During the day, this is usually done with fill-in flash or reflectors.
Therefore, a practical solution is to wear a white t-shirt, which will reflect the light from the flashlight towards the subject of the picture. This will not fix the lens flare, but it will light the subject better, and it is plausibly deniable and inconspicuous.
However that requires you to be perhaps closer than you would like.
The other solution is to have friends, which means having more cameras (and witnesses) than there are flashlights.
You could also play with the camera settings to decrease contrast, to make sure dark areas are not pure black but still contain usable detail that can be recovered via post processing. Perhaps use night mode, or manual mode.
Using the highest quality setting and lowest compression will help.
Another thing you could do is simply hide the phone.