Hello, I'm Dr. Ralston. Thanks for your question.
This doesn't sound like swim bladder disease, although there are some parasites which can spread that can cause this. They tend to float, have troubles regulating depth, and might even have a buldge on the side.
I'm willing to bet that your fish act lethargic most of the time and lay around, but when you add feed they jump right up and eat it energetically, only to go back to the way they were before.
Aquasafe is a conditioner to remove certain minerals from the water and chlorine. But, that's not the problem here.
I need to ask you some questions.
What was the nitrate level BEFORE you replaced the water (40%)?
What was the nitrite level BEFORE?
And what were they after?
Replacing the water is a good idea. It doesn't FIX the problem either. It just dilutes the problem
There is a bacteria in the pond that is converting ammonia from the fish into nitrites which are then broken into nitrates.
It builds up overtime naturally because the fish are in a closed system, and they eat and then excrete wastes. Bacteria convert nitrogen (ammonia) into nitrites. Nitrites then become nitrates. Normally plants then clear the nitrates out of the pond and convert them into energy. But, if there aren't enough plants, the nitrates build up. Have you had a recent loss of plants? OR, are there more fish in the pond than before?
There doesn't need to be more fish than before to make more waste product. You could also be over feeding them, or the meal you are giving might be higher in protein and thus causing more ammonia to form. I would consider that.
If the fish are very sick, you might need to replace about 20% of the water per day for several days in a row until your nitrates and nitrites are back under control. I would aim for less than 0.25 ppm of nitrites or LESS. Ideally it should be almost 0 if the system is in balance. NITRATES should be between 20-60ppm. No system will be 100% nitrate free in the water. It's because the fish are always making more ammonia and it's always being converted to nitrate...
Nitrate levels above 80ppm and you need to start changing out the water routinely to keep it lower than that. Anything about 120ppm and your fish are going to be sick. Really sick.
Are your fish gasping for air at the surface? Or are they hanging out near a bubbler? Or fresh water source? Air stone? ETC? The high Nitrates will eventually start to burn the gills, and affect the respiratory system. They can't breathe well so they get lethargic. Their blood becomes brown as hemoglobin can't carry enough oxygen.
SO, to be clear, you must be sure which is high.
If NITRITES are high - you need to add bacteria - Nitrosomonas. You can get these online or in fish supply stores. There are several products.
If NITRATES are high - Cloudy water, a sharp odor, scum floating across the surface and algae blooms are indicators that ammonia or nitrates may be building to unsafe levels. You need a filter. A biological filter is a good idea. Also remove any dead or decaying plant material and you will need to consider adding some new plants to the pond to break down those nitrates.
But definitely clean out any dead leaves in the bottom, and try to clean out that gunk that builds up on the bottom. That's where the poop is going to go, and that's where the nitrates are being formed. Skim the surface to remove any organic stuff like leaves, or grass, or algae.
And, most likely you are over feeding. Especially if there is food left on the surface of the pond after 5 minutes, or you are seeing it down below on the bottom. If the food is staying long enough to soak and drop to the bottom, it's too much. Now, when they are sick they might not eat as much. So, the food will build up faster. Once you get the nitrates down from water changes, they should start to feel a little better. You might have to change 20% per day for 4-5 days. After that you will definitely have to add some new bacteria.
Also, if temperature is low, like 50's most of the time or less in the winter, you really only likely need to feed every other day. Fish metabolism slows waaaaay down.
A note about testing - test the water at the same time every day. Levels change during the day so, test at the same time to be consistent.
If after changing out the water for several days, and after getting the nitrates (and nitrites) back to normal levels you find that the fish are not recovering and the nitrates are building up again -
1. you need a better filter system
2. you need to consider if you are feeding too much ( all food gone in 5 minutes, none of it soaking and sinking to bottom, in winter only every other day until it warms up to the 70's)
3. is that pond clean as a whistle? If there is plant gunk, green gunk, dead leaves, decayed stuff in the bottom, get it out of there.
4. add more plants to help convert the nitrates
5. consider overpopulation and consider reducing the number of fish (the two dead actually might help the system overall). Again, they might not have increased in number. But they are probably increased in size, especially if over feeding is a problem. The bigger the fish, the bigger the poop.
Anyway, I hope that all helps. Off the top of my head so a little rambling. I apologize for that.
But, once the pond is clean, the fish will feel better.
Please follow up with questions.