I don't understand that question - change a lightmap? You simply have to assign an other lightmap textue to the second coords set of the meshs UVs. So tell the texture to use the second UV set with
Texturecoords tex,1
and assign it to the mesh:
Entitytexture mesh,tex,0,1
To save the mesh with the new lightmap you can simply replace the filename in the file, or use a B3D Mesh exporter that will handle lightmaps. In that case you need to define the brushes with 2 Textures, where the 2nd will be the lightmap for all brushes. the blending mode must be 2 if I remember right and the entityFX must be 1=fullbright.
Texturecoords tex,1
and assign it to the mesh:
Entitytexture mesh,tex,0,1
To save the mesh with the new lightmap you can simply replace the filename in the file, or use a B3D Mesh exporter that will handle lightmaps. In that case you need to define the brushes with 2 Textures, where the 2nd will be the lightmap for all brushes. the blending mode must be 2 if I remember right and the entityFX must be 1=fullbright.