So, I have done this baking a few times now and not sure what is causing the problem. After spending a few hours baking my scene, all lightmaps seem good, I created a custom lightmap folder also. Soon as I hit play in Unity, all lightmap data is gone, the custom folder still has the map data, but my scene is back to no mapping data.
This has been a huge waste of time, and I need some advice as to what’s going on. I don’t remember this happening in the past, so I’m not sure whats going on here.
Every time you bake lightmap, your previous lightmap asset gets removed. So maybe (just maybe) Unity re-baked your scene and all the lightmapping data (which is in a folder in the directiory that the actual scene is) got deleted.
To be honest, I don’t think Unity3D is ready to handle huge scenes out of the box, yet.
However, if you use older versions of Unity that use Beast instead of Enlighten, then it might be possible to have all the lightmaps data in a scene every time “Bake” button pressed.
I believe Enlighten does the lightmap assets management job much better than Beast, though.
Have you pointed the GI Cache to be inside your project folder (I am looking at BakingScreen-Capture02.JPG)? This is not a good idea since hitting the bake button will clear the folder that the lightmaps are stored in and therefore invalidate the cache… Please make sure your GI Cache is outside your project folder. http://docs.unity3d.com/Manual/GICache.html