Now that I understand what you are working with, I can suggest this workflow.
Your main comp should contain the grunge layer on top, the light effects or light flashes layer below that, then the background footage.
When you have the composition arranged that way, and you are satisfied with your Lightning layer, you need to duplicate the layer, then pre-compose it moving all attributes to a new composition. Name that Pre-comp Flashes for now. Open the new Flashes comp and select the layer or layers that create the flash and scale them down until they are about 200 X 200 pixels. Add Gaussian Blur and maybe levels so that the pulsing bright pixels come close to white if you can get them there.
Back in the main comp, turn on the top Grunge layer and add this expression to Opacity:
ref = thisComp.layer("Flash");
clr = ref.sampleImage([thisComp.width/2, thisComp.height/2], radius = [100, 100], postEffect = true, t = time);
t = rgbToHsl(clr)[2];
linear(t, .1, .78, 0, 100)
The expression looks at a 200 by 200 square in the center of the comp and creates a variable "t" for the luminance value of the average in all the pixels in that area. The linear method will animate the opacity of the Grunge layer from 0 to 100% as the luminance value increases. In the sample comp that I created .1 was a good starting point to give me 0% opacity, and .78 gives me 100% opacity.
The last step is to change the Blend mode of the Grunge layer to Add or Screen so the lighter parts show up on top of the original image and the lightning. I just used some Optical Flares and a solid layer to demonstrate opacity changes controlled by average brightness of the scaled and blurred pre-comp.
This is the pre-comp:

This is the main comp:

You should be able to get your comps to work if you follow this workflow.