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Andrea, you are absolutely right that breeding to a blue eyed white would be your best bet. Since blue is recessive, there's a far better chance for the brown to show (though it may result in one blue eye and one green eye).

She's an awfully pretty girl, even if her feathers don't turn out to be buff. I've seen ducks with one eye that was half blue/half brown... but I can't remember one with one blue and one brown. Since she's a combination of black and white (literally, if you bred her to another bird with her...

Give the chickens a round of antibiotics and some dewormer "Just in case"? If there's no nasal discharge or sneezing it's unlikely that they'll spread anything airborne. I'd be more concerned of any possible droppings.