Ahh, i just tried blacking out the base shading layer and then re-copying the channels, that seemed to work. That problem is solved i guess.
Ok now as to my other request, optimisation. My exact workflow currently is:
Alt+left click the vector mask of the layer (sclera to start with)
Press Ctrl+A to select all
Press Ctrl+C to copy it all.
Left click on the top (baseShading) layer
Click on the Channels tab
click on the destination channel (red to start with)
Press Ctrl+V to paste
Click back to the layers tab
Repeat the above steps another three times, once for each other mask, with destinations as green, blue and alpha appropriately.
Is there any way to speed up or automate this process? Perhaps even writing a script? if i could just give her an export script to run it'd be simpler 
If you're all wondering the exact point of all this, we're making a game with user customisation via tinting textures. I've written a custom shader for unity that takes a colour mask image, where the masks for tinting of the texture are encoded in the RGBA channels of the color mask image.
The reason we have it in layer masks to begin with, is for design and previewing purposes. it allows us to see roughly what the final result will look like ingame, without having to export and test it for every tiny change, and provides a visual environment for carefully adjusting how the channels blend.. What i need help with now is just making this exporting process simpler and quicker.
