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I do not see where containing and mitigating known issues, and potential issues, with chickens on the OP's property is giving up their right to have chickens, or gives up any rights at all. If the chickens were causing damage to the neighbor's property, then the OP is liable for he damages. If the birds are running up on to the deck and then leaving deposits, it is no different than a dog or a cat doing the same--and there are plenty of nuisance complaints caused by free-roaming dogs and cats.
So, my point is that if you know that you can have a rooster crowing at 4:30am, because of light from a passing car, then you mitigate that by limiting the light that can get into the coop at that hour. Because, IMO, if the neighbor is already causing problems, why not think two steps ahead and limit what they can legitimately complain about? Certainly, if you can not only prove that you've taken reasonable steps, and can get al the officials to agree that you have, then they are more, not less likely to do an administrative roundfiling.
My argument is that once the OP establishes themselves as someone clearly practicing Due Diligence, and the officials all agree on this, then there is only so much power that a disgruntled neighbor making anonymous calls has. IMO, until this individual has to out themselves and demonstrate actual harm caused by the OP's chickens, so that the matter can be finally decided, the OP A) has already lost a lot of their rights because the anonymity of the complaints guts their right to Due Process and Facing their Accuser, and B) it's going to continue to be a death by 1000 cuts. Due Diligence, especially when you carefully detail it, is a powerful weapon in these kinds of situations.