I see all my lightmaps in the editor, but not on the device. Any surface that is affected by a lightmap is totally black now. Like when the bug with the mobile/unlit shaders was present in 5.0.
I’ve stopped saying “there’s an update”, and started saying “lets see what’s broken now”. 
And i did rebake them after the conversion.
Sorry for bumping this one, but did you find a fix for this? I’m having the same issue on unity 5.1.0f3
edit:
Logcat is full of this:
GI: material does not have Meta pass, and could not find default material. Object will not be affecting GI
edit 2:
fixed by disabling multi-threaded rendering.
Unity QA said that my bug report is to be fixed with 5.2.
What it take 2 months: http://unity3d.com/unity/roadmap
Sepetember, you got be joking me, they need fix this in a patch…