Just started watching a few threads here, been a busy, busy spring. Let me help out.
My gut feeling is the problem is with the original fish. I think something happened with them during the handling process. Delayed mortality isn't necessarily normal, but I've seen it happen. Here's an example: If fish are held on a truck too long, or in an oxygenated bag too long, there's an ammonia buildup in the transport water. Their gills are burned, and their metabolism is affected. Left in that water too long, they die quickly. But, I've seen fish before, tempered and stocked before they died on the truck, only to have some rapid mortality in the pond, within a few days. The other fish begin to heal, but with consequences. They're still "sick" because they can't fully recover unless all their stressors are gone. When the water temperature rises into stressful levels (above 84), their metabolism rates are affected and so is their ability to take up oxygen through damaged gills. When their metabolism revs up, they need more oxygen. On rare occasions, I've seen fish die a week, two weeks later, with a few lingering fish giving up within a month. I know this case fish have died later than that.
The fact that the supplier replaced the fish is a noble gesture, regardless of the cause of death. One question I would have asked the supplier is, "Did anyone else on this load lose any fish". If they're honest, which we presume they are, they'll answer. That gives a lead into the "problem".
Regarding ammonia being the "problem" here...there's got to be a source of ammonia in high enough levels to cause that to be the problem. It's common practice to stock a brand new pond immediately to make sure our stocked, desired fish gain a foothold before nature (or the friendly neighbor with stunted bass) stocks it for us. The only time I won't stock a new pond is if it is loaded with terrestrial vegetation that I expect to decompose rapidly. Then, we'll wait. Bluegill the size of the ones in the picture weigh about 15 per pound. That means less than 20 pounds were stocked. That mass of fish won't influence water quality.
If the fish haven't been the "problem", then there's something else besides ammonia causing water quality issues. After this much time, especially with aeration, the pond should be settling down.
My gut (and 40 years experience) suggests things will settle down, remaining fish will reproduce and the pond will be fine. If not, there's something else going on with the water that we don't know.
