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Just my 2 cents worth,I've seen a lot of poorly feed amazons and haven't noticed the brown spots. The brown color in some amazons usually comes from the red clor mutation in some birds, as you know the green color comes from a mix of blue and yellow. In some birds the blue is replaced by red hence the brown color.Aging and molting will change the color of amazons ie; your YN 's nape getting yellower with age because of loss of the blue color. this may be related to your bird losing the brown spot or red pigment , i would not be surprised if this spot turns yellow many years from now..