Why is it that you think that flashlight use may be the cause of your low grade headaches?
I agree with inetdog. PWM stands for Pulse Width Modulation. The LED is turned on and off very quickly; that produces some flickering, in some lights, and some people are very sensitive to it. Typically, though it is more pronounced at LOW Levels of light, ( the opposite of what you describe for your symptoms). Years ago, I recall reading that some people have problems with florescent lighting. I don't recall if it was due to flickering, or color temperature. Without white light balance, photos taken in florescent lighting may have a greenish hue, or a pinkish/tangerine hue, depending upon the phosphors in the tube. I believe the solution was to change to "full spectrum" lighting.
IF... nothing has changed, except that you now use flashlights often at work, and you can assert that this is what brought on your photo-sensitivity. Let me propose this.
When in bright lighting, whether it be sunlight, or artificial, your iris will "stop down" to reduce the amount of light that hits the retina. The iris closes with muscular contraction. Perhaps it is getting too much exercise. OTOH, perhaps the type of beam of your flashlight is the problem.
A floody beam is typically better for close up work, if you are using a light with a tight hot spot, up close, there may be too much glare for your eye to compensate. You may do better with a more floody light, or with a more warm color temperature light.