I have come across a very strange issue with the lights in my level. Whenever I try to bake the lights, some of them vanish. It is acting as if Unity doesn't like have multiple version of the same light type. In my previous project I had several spot lights dotted around the environment as I had lap posts. and I have had this problem before.
I'm not sure if it is due to a bug with this version of Unity, as I have not changed any settings for lighting or for the project. So when I get back to my home version of Unity I can test it on there.
Update: I had tested baking at home on a newer version of Unity and for some reason I got the same result. It is very strange as when I bake they dissapear, but if I were to move the light source slighy with auto bake on, it sometimes re-appears, then if I move it again it goes. I will have to spend a while trying to figure out whats wrong and how to fix this; and if all else fales I will need to make a new scene and piece together my envronment.