I am on the board of my HOA in an upscale suburban neighborhood. The first thing I did before getting hens was to read the fine print in our CC & Rs (Covenants/Codes & Restrictions). Ours says:
"No animals other than dogs, cats, CAGED BIRDs, tanked fish, and other conventional small household pets may be kept on lots"
I personally will interpret caged birds to mean my chickens would not be in violation since their chicken run is a large cage. It did not specifically say "INDOOR caged birds". If people wanted to be really picky about the "tanked fish" part, people who had water features with koi (those large goldfish) in their backyards would also be in violation, but who's going to complain about a backyard fish?!
So lucky for me....I think I'm in the clear with the HOA, if only my chickens didn't violate county zoning laws! Shhhhh
Anyway, back to your issue, as someone on an HOA board who has to deal with CC & R violations, I can tell you that our enforcement powers are pretty darn weak. We can send all the letters we want to violators, and fine homeowners all we want, but without official legal action, we can't really make anyone comply or pay. We are extremely hesitant to go so far as to hire a lawyer to bring legal action against someone, because even though the homeowner (if they lost) would have to reimburse the HOA for all legal costs, it would cost the HOA a lot of money and effort upfront to initiate the whole affair----which none of us wants to do!
I guess what I'm saying, is that if your hens do not garner any noise/odor complaints, and if the only reason you were sent the letter is because someone else's roos were making a racket.....do nothing. Maybe you'll get lucky, and the roo owner will get rid of their roos, no one else will complain, and the issue will go away.
Best of luck in the whole situation! I'm a first time chick owner of 4 week old Ameraucanas, and I know how totally attached a person can get to their "pet" chickens!
-Michelle