In your code, cycles through your lightmapped meshes, for each one assign the corresponding lightmap texture to the lightmapTexture property (in gltf, a mesh can only have one material), don’t forget to tweak the coordinatesIndex (0 = UV1, 1 = UV2, etc).
It’s the same logic than in my tutorial linked above, but adapted for gltf convention. Of course your assets naming convention have to be robust.
Maybe by using the BJS Blender exporter which used .babylon format you may even doesn’t have to modify my tutorial code (not sure, haven’t test yet).