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Comments
I am not sure whether I understood correctly what you were doing. If you duplicated the eyelash and selected only the new duplicate layers and gave them the hair mesh ID for clipping, it should only clip these parts to the hair. If you then clip another layer to the already clipped layer it will show completely, because encapsulated clipping or "double"-clipping is not possible. One way to fix this would be merging the layers. Generally to create the effect of double clipping, you can also use the "invert mask" feature to do inverted clipping. There are tutorials out there explaining this method. How did you use a second layer to "color" the eyelashes via clipping? Maybe you can achieve a similar effect by applying the coloring options to the copied eyelash layers? Try multiplying with a pure black then changing the screen color to the brown hue you want. For the semi-transparency you can then adjust the opacity. I hope this somehow helped.
Best regards,
avi