Does anyone know whether or not it’s possible to import a secondary UV channel in the 3d model to use for baked lightmapping? I’ve created a secondary UV channel in my Blender model, imported the model without selecting “Generate lightmapping UVs”, however in the lightmapping atlas the charts seem to overlap itself when trying to not have Unity generate lightmapping UVs. So I am wondering if this is even currently possible in Unity 5.2.
thanks
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Baked (NOT realtime) lightmapping should respect the UVs.
What you are describing should work.
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j
In blender, the secondary UV channel was created. It was imported in Unity. However, in the LB atlas it has overlapped itself, as noted by the blue line from the diagonals. With generate UVs seletected, the mesh appears fine in the atlas though.
With generate UVs, it is fine:

j
see my latest reply, i have a screenshot.
How does the other channel look? (Is there a chance the UV channels are swapped and that’s the 1st UV channel we’re seeing in Unity?)
Channel 1. It is messy, but the unwrap is custom.

j
I figured out the problem. I had one of the large planes hidden in the Blender model (ALT+H), therefore it wasn’t being added to secondary UV channel properly. User error.
After correct lightmap pack in Blender:

I lost track of how many times I have burned my self by hiding meshes in Blender, and forgetting to un-hide them. 
j
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You saved me, I’d also hidden some mesh. How ridiculous ^^’
Thank you for sharing that afterwards!
can you guide me , how you’ve assigned seprate channel of UV for Lightmap baking in Unity ! ( I’ve porps with 2 UV channel 1 with texture and other empty channel for Lightmap )