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Inspectors can be wrong. It helps to be polite and respectful with them because they invariably believe they are right and they can make your life miserable if you cross them. But they can and do make mistakes. Do not get rid of any chickens or make any substantial changes to your setup until they have cited you for a violation AND you have exhausted all appeal processes. They may never cite you for a violation. In which case you have no problem.
In the meantime, do some research. If it turns out your coop really is in violation of current codes, find out what it would take to get a variance. If you are on good terms with all of your immediate neighbors and they are all supportive of your project, it is much easier to get a variance. If you are not sure how they might stand on that issue, now is the time to ply them with fresh eggs. Before you have to ask for their assistance.
It is nearly impossible to get a definitive answer out of a government employee when it comes to finding out if a specific setup meets current criteria, unless they have an application with plans and specs in front of them. Even then it can be difficult. They know that whatever they say is going to come back and bite them. So they don't say anything. On the other hand, they should be able to tell you which rules, regulations, and codes apply to your situation. You just have to find the right person to ask. That may take some time.
I hope the 9 square foot maximum coop size you mentioned in another post is a mistake on the inspector's part. That sounds dangerously small. I can't believe the city would limit coop size to something that small. It would be an animal welfare problem for anyone with more than a couple of hens. He might have meant that you needed a building permit for anything larger than 9 square feet, which doesn't really have much to do with it being a chicken coop. It would be an unpermitted structure.
Good luck. And keep us posted.
(Edited to reposition some of the paragraphs, which managed to get out of order in the original post.)