All I can offer is a few possibilities for you to consider.
From my own experience, I think that if low oxygen during the change was the problem, the larger Koi would have been effected first, before the smaller ones. But when a toxin is in the water, such as chlorine or chloramine, the smaller ones are usually more sensitive and affected sooner than the larger ones.
I have been told by people who run chlorination stations that the amount they add is varied with the local temps and rainfall levels. Houses closer to the treatment points will have higher levels of the treatment added show up in their taps. This more true when chlorine is the additive used, than with chloramine, as the latter is more chemically stable.
Two other thing to consider, but may not be all that likely due to the amount of water changed is the fact that water from the tap can have VERY low oxygen levels, and the pH can be quite different from the pond water.
An afterthought, water temp differences can also severely stress the fish, but once again, with a small water change, it would probably not be enough of a change to make a difference.
Wish I could offer something more concrete.
Mike S.
Spring Hill, FL