Hi, E Ellis, so sorry for your loss! As others have said, I had a large goldfish kill 2 year ago. They sprayed the soy bean fields that literally surround my property with airplane. The farmer said no way the fungicide would have caused any fish deaths, but they also were not aware the plane sprayed directly over my whole yard! I realized THAT fact last year, when the same company spread fertilizer pellets over the corn, and spread it over my entire yard, including my ponds. The fertilizer caused no problems.
It's my best guess that the chemicals are what have caused your problems. As I learned 2 years ago, there are specific chemicals that are deadly to goldfish, but koi are not compromised at all. I have a koi pond and a goldfish pond, about 15' apart, but the water does not get circulated between the ponds. So, the water is separate from each other. Only the goldfish died, didn't lose one koi. I researched as best I could with the chemical "ingredients" and although there were words that were roots or endings that were similar to the type of chemical I was told was possibly the culprit, we never were 100% certain that is what it was.
The good news is that after about 10 days, the dying stopped. I lost about 25 goldfish, all sizes. Some of the largest ones are still doing fine, and some of the small ones are growing up. No clue why it targeted some and not others. It sounds exactly what you are experiencing, though.
I guess this isn't giving you any real hard proof of anything, and I apologize for not remembering the name of the chemical that is known to be deadly to goldfish but not harm koi. I am going to send a private message to Dave 54, as I believe he is the one that told me about the specific chemical.
The farmer that farms the fields near me is great, and we are working together, and they are supposed to let me know anytime they plan to spray, but once I had proof the plane was not shutting off the spray or fertilizer going over my yard, that to me was a big indicator that the chemical 2 years ago caused the deaths. The pilot and that company have been warned! The fact I had fertilizer pellets on my back deck, and all over my yard, but not over my horse's pasture was proof enough for me! They sprayed field across the road from my house (the pond is in the back yard, road is in front yard), and on all 3 other sides of the house. I stepped it off, and IF they had not sprayed the yard, they were still closer than regulations recommended for the chemical for "running water". They didn't think of my pond as running water (like a stream), but it has living fish in it, so needed to be considered that way.
Again, I'm working with them, and they are working with me. We will get it figured out like good neighbors should. Good luck to you! I hope the dying has ended, and your fish will come around in time.