It would help if you could get a photo or two so we can see what you are talking about. Some bays get dapples, my mare had them, but they are normally associated with good health and a short summer coat. He could just be growing his hair back in patchy, and in a different shade then you are maybe used to, though he will look the same once he's regrown his coat. Different foods, change in diet, change in the quality of hay, ect., can effect how his coat looks, and how it grows. Again though a picture would be extremely helpful in seeing what exactly is going on.