selecting the part of the hair you do want coloured in on the mesh, and then exporting the uv map for that area. You can then place the map in a layer on top of your texture in whatever program you're using and just colour in that section. (Sorry if this doesn't make a whole lot of sense; I'm a bit tired.) There should be a recolouring tutorial out there that covers how to do this, but I couldn't pull any up when I searched.
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