Excellent - I just tried it out and yes, two skyboxes worked fine.
One needs to be night and the other day, so I may dispence with the sky lighting entirely, and just set up some invisible light emitting brushes to mimic the two required sets of ‘lighting’.
one thing you can try althoug could be complex. i am asuming there is some distance between your two skies probably a large indoor area so the effected lightmaps for each areas are probable quite seperate on the ligthing images.
compile with sky light setting, compile with the other sky setting then swap and chop your lightmap images so you have the right lighting in each area. only thing is though pretty much every change you make will demand you do this so you might want to run some tests then on the final versions put the effort into chanaging the lightmpas around.
im not syre you would be able to get the desired effect with light emiting shaders as i dont think you can specify direction and a directional light wouldnt give the nice parralel lines you want from a sky. also to get the lighting area big enough would involve turning the light value up to some serious numbers resulting an washed out lighting