Maximum gallons of pond would be 5,000. Shelving and internal structures take up volume and makes the pond closer to 4000 gal maximum and probably less.
You stated above: "but this time we counted the amount-it turns out we still have 178 fish.... but then there are 50 less". This calculates to now about 128 fish. If you have 4000 gal, each fish has 31 gallons of water. This is not alarming if the fish are small such as 2"-6", but if the fish are larger then it becomes a big concern. Example: 10 6" koi are the equivalent biomass (waste producers) as one 12" koi. One 20" koi is eqivalent to 5 12" koi. 100 1" fish are the biological equivalent of 1 6" koi or goldfish. Readers should get the idea. I think 128 fish larger than 6" with some being 12" or longer, is too crowded for a healthy fish enviornment unless you are providing intense aquaculture conditions. Aquaculture conditions require daily monitoring of vital chemistries and iintense mechanical and biological filtration.
Many backyard ornamental pond people have the "stamp collector" mentality when it comes to fish. This view holds that the value of the hobby is directly related to the number of fish owned rather than the quality of the aquatic habitat provided. How many dogs and cats do you have to own before you consider them worthwhile pets? Is 128 too many? High fish loads means high bacterial loads. High numbers of bacteria puts a greater burden on fish immune systems and this increases the chances of bacterial infections.
One water quality issue not previously discussed are DOCs - dissolved organic compounds - that are a host of carbon based substances that exist in pond water. The main ones of concern are those dissolved substances derived from metabolic and biological byproducts such as fats, proteins, amino acids and so on. These substances have an insidious impact on fish health and are linked to disease causing bacteria in pond water. Ornamental ponds with dense fish loads are notorious for having unusually high DOCs. Best way to reduce DOCs is maintain low fish loads and occassional water changes.
I think all your problems with fish deaths will relate back to too many fish for the water quality within the pond.
Most importantly when one is dealing with a backyard ornamental pond, it is not so much the number of fish per gallons but one has to carefully consider fish biomass per gallons. Can you provide an estimate to us of what sizes of fish make up the 128 remaining fish in your pond?
I suspect that your pond does not have enough plant life to properly biologically filter the water to maintain its quality. Each 12" fish (abt 12oz) should have 112 ounces (7 lbs) of living plants (emergent and or submerged) in the pond or in an external filter for proper biologicial filtration.
Lastly it is important to realize that as fish grow, one should not add fish but remove fish, from the ornmental pond to maintain proper fish load balance. Example, you might have 36 4" koi in a pond today. But when they reach 6", the pond is overloaded and 27 fish will have to go. This assumes that the pond is properly maintained and receiving adequate aeration, and mechanical, chemical and biological filtration. To determine the maximum safe fish load for a backyard pond divide the gallons by 100. The answer is the number of 12" koi the pond should support. Remember, when the fish grow, one 24" koi is equivalent to 12 12" koi. I have tables and charts that provide fish biomass equivalents.
One last thought, I think is was a mistake to put all your fish back into a newly cleaned pond. The entire old fish biomass will create way too much ammonia and other waste products for the cleaned ecological system and the biological filtration to "handle" or process and your water quality will suffer until the fish biomass is reduced to safe levels (deaths) and/or the biological filtration re-establishes itself to the point it can handle the fish bioload.
