Finally found evidence that the baby koi are dying... well, I found one baby koi floating, anyway. There's only one in the small pond which makes an appearance from time to time, but it's not to eat. I'm thinking that if the others have died, they must have gotten tangled amongst the plants; either that or some birds are plucking the corpses from the water. In the large pond, I still see a couple of the babies swimming around, but haven't noticed any other bodies.
All of the bigger koi are doing just fine. They seem to adjust to water changes easier than smaller ones. All four of them are swimming in a school with the three goldfish that remain. The goldfish are between 6 and 8" long, and the bigger koi are about the same size. So they seem to school together better than the little ones.
Okay, time to get some sleep.