Hello; The fact that some of the fry are alive after this amout of time in a good sign that the water is not toxic. I have had the experience of not seeing fish that swim near the top of the water.
The trick is to keep a balance between adding new fish, snails, shrimp and such and the size of the bacterial colonies that will consume the excesss ammonia they produce. My guess is that whatever happened to the missing fish had little, if anything, to do with the water quality. My experience with fry has been that many just do not make it very long and that a good number do not make it to a size where they can be released into a community tank. I mainly have raised egglayers and have seen up to near 50% loss or significant deformities by the time they reach maturity with several broods.
My understanding is that the beneficial bacteria (bb) will reach a population that is basically dependent on the amount of food (ammonia products) available. They can reproduce very quickly. One old thing that stuck in my memory from microbiology is that a bacterium could multiply under ideal conditions to a mass the size of the earth in 24 hours. Colonies are self limited by natural restricting circumstances to about a dime to quarter size. This seems to me to indicate that the populations can expand to new additions in a tank quickly.
Adding filter media loaded with bb a week or so ahead of the new fish should lead to a crash of the population of bb unless a food source is also added. I suppose this is fixed in a fishless cycle by adding the dead shrimp or pure liquid ammonia. It also seems to me that throwing objects (media ,substrate, ornaments, plants andother solid stuff) from an established into the new setup about the time of adding new fish should help as the objects will have the bb on their surfaces. I have gotten into the habit of adding plants and snails from an established tank and stocking the new setup somewhat slowly.
Again having live fry that survived to this point is a good sign. The missing may have jumped or are still hidden or something.
As a further point, so far every single pet fish that I have ever kept over 5+ decades has died. Some way too soon. Many within a year or so. A few have lasted for many years. I currently have some tiger barbs and zebras that are at least four years old right now. Two observations. One is that we, or our paid agents, take these fish from their natural habitats and put them into artifical and likely very much less suitable containers for our entertainment. I have moved over time to keeping only tank raised fish for the most part so as to contribute less to the wild fish trade slaughter that is going on. Even so any one who keeps fish in a tank for his/her pleasure is an enabeler to some degree.
Another is that many of my fish have lived much longer lives without hunger or predation that their wild cousins.
I am too selfish to give the hobby up for humanitiarian reasons. Overall, fish keeping has some unplesant aspects from poor quality fish stores, poor techniques of capture and transport on the comercial end, folks buying or raising feeder fish to the huge commercial practice of culling non-comercial results of inbreeding so as to present us interesting new varities. Most of us bungle our setups from time to time and cause the death of fish. It seems to me that we fishkeepers are all involved in this to some degree.
This forum might be better served by trying to help fellow fish keepers solve the problems they face, than taking a jab at them when some problem shows up. Each of us gets to keep our tanks whatever way we choose in the end.