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update v2.0 Added codes to disconnect lightLinker1 from initialShadingGroup. And restoring shading group connections to lighLinker1.
If you are having trouble saving file which took like 3 hours to save. Chances are the light link bug. Try this script. It might help. Just open the maya file and run the script. If you are using reference file. Run it on the referenced file. Not on the file that is referencing the referenced file. (lol) Otherwise your file are gonna get bigger because of the added commands on the reference node.
p/s anybody knows how to re-produce the light linking bug?