I've recently read up on how the lightmapping works and it has come to my attention that the truth is a bit more complex. Unity uses UV2 (or uv1 if there is no uv2) combined with the lightmap scale and offset to calculate it's lightmap uv. It then looks at the lightmap index to make a look up into the actual lightmaps as part of it's lighting model. The FBX format does not support lightmaps in a similar fashion so while I could export the data, no importer would read it properly. I will add functionality to allow exporting the lightmap textures along with either the modified uv2 or a data file containing the offset and scale so that this information is available when importing the fbx.