The snippets you posted really helped me out, thanks!
I needed to get it working with the “Lighting.j3md” Material and based on what you posted figured out how to combine both baked lighting and a directional light:
Material mat = new Material(assetManager, "Common/MatDefs/Light/Lighting.j3md");
mat.setBoolean("UseVertexColor", true); // activates our custom colour lighting
The key was setting the UseVertexColor boolean flag to true, which activates the Color buffer. My next task is now to work out how to create two Color buffers, one for night, and the other for day, interpolating between them on the GPU. I guess I’ll need to fiddle around with the shader code to do that.