My use case is baking light into prefabs, which I do using an editor script to pack all light related data (maps, scene environment, light data, etc), and unpack it in realtime using another script.

This works wonderfully in 5.5, but because in 5.6 Light.bakedIndex is deprecated, I cannot control whether a specific object is already lightmapped, therefore causing overexposure when placing the light baked prefab into a new scene with dynamic lights.

A straightforward solution would be to make sure that objects that have their Renderer.lightmapIndex set to anything other than -1 will not be lit by mixed/dynamic lights (perhaps the original intended behaviour?).