I'm referencing the technique from Yibing Jiang's Siggraph course from Uncharted 4. Slides can be downloaded here:
http://advances.realtimerendering.com/s2016/On slide 45 you can see the technique: Basically bake an AO map from UVset 1 with alpha transparency onto UVset2 with cards fully laid out to get a shadow map.
Maya will not take into account the transparency, neither will Xnormal or any other bakers I know of other than 3DSMax. Had anyone had success doing this with Maya or any other bakers?
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In Maya, use Windows>Relationship Editors>UV Linking, and UV-Centric. Here you can link a texture to an object(s) uv set as an override, to say "this texture should be active on this particuar uv set."
(i was going to post a pic, but my ISP seems to be having issues today)
Quick edit: I just realized your issue was in baking, i think. In the case of Maya, you can select a uv set to use in Transfer maps