A couple of observations and thoughts here. Though its now water over the dam, you did not Q the fish correctly. So let me start with this.
Quarantine can mean different things to different folks. However, the first consideration in doing Q depends on whether one is dealing with wild caught or tank raised/farmed fish. How long one Qs is based on this. For farmed/rank raised the period is 4 weeks and for wild caught it can be up to three months. This has to do with what problems one might encounter and how long some things can take to manifest. I usually use 30 days for domestics and 60 for wilds. However, these periods do not mean total time, but rather they mean consecutive days with no illness or symptoms.
This means if you have a fish under 60 day Q and it gets sick after two weeks and it takes two more weeks for it to be cured, That the 60 days restarts from the time it is cured. Assuming no further illness the Q in this example would have taken basically 90 days, not 60. Applying this to your loaches, you can see they were not left in Q anywhere long enough.
Next, loaches almost always live in groups and these have a pecking order. When one puts a new group into a tank it can take weeks if not a couple of months for them to work out the pecking order. When loaches are fighting they tend to do a lot of heavy rapid breathing. When the smaller ones are stressed by the bigger, the will breath rapidly. So this is often not a sign of illness. The same applies to fading. This is often a sign of submission. It is also a sign of stress. You will also find when they sleep, they may also fade. All the fish will fight since number must contend with number 3 and so on down the line.
Loaches are not happy about being medicated more often than not. So this can also affect them during that time. Yours have been subjected to almost continual medication since you got them. So they are clearly under stress from the meds not to mention anything they may have cured.
If you have velvet or ich, the Flub. is good for that and when I have used it with my clown loaches, they were not overly bother by it, but were not quite their normal selves.
From all I have read about your issue, I cannot say I am convinced that the fish are actually sick. Hiding, is notmal, some rapid breathing is normal, they are eating normally as well I think. Ich would be pretty obvious in not much time, but velvet/odinium might not show up so clearly. However, Flub. should be good for both. However, I cannot say that your fish are fine for sure either.
Antibiotics used in combination with other meds can cause some issues depending on which ones are being combined. And this might be the cause of some rapid breathing.
Another consideration here is that gill flukes can be hard to diagnose as noted below. Here is a quote from the fish disease section on Badman's site regarding gill flukes:
No photos are included here, because usually flukes are too small to visualize with the naked eye. This also creates serious problems for trying to diagnose by general physical signs (hyperproduction of slime, inflamed gills) or general behavioral signs (listlessness, gasping, scratching, etc.). All these signs overlap considerably with other more common causes of skin and gill irritation, including ammonia poisoning and more common skin parasitisms such as ich. The first step in any tank where these signs are seen is to rule out ammonia poisoning first by testing for any level above 0.
from
http
/badmanstropicalfish.com/fish_palace/tropicalfish_disease_identification_1.html#Fluke
This opens another possibility. While your one test reported in this thread showed ammonia at 0, it was only test and the symptoms have been there a while. So it is possible you had ammonia but it was finally gone by the time you did test.
Loaches tend to bolt for cover and hide during water changes. They are being stressed during this time, so even though one adds back clean water which would normally mitigate certain issues, when you are done and the fish come out they may be breathing rapidly because of the stress factor which can also explain fading at times.
So what I see is both the possibility that your fish are not ill but are merely adjusting to a new tank, a new grouping and a bit of stress. It could be that they did have something in Q which was cured, but maybe not eliminated and it has recurred. You may want to consider holding off an throwing more meds at a problem which might not exist. If there are flukes or velvet/ich in the tank, it seems logical that some of your other fish should also show some symptoms.
The difficulty is I cannot tell you that your fish are not sick with certainty, only that they may not be in as bad a condition as you think or may be completely fine as much of what you describe can be attributed to normal behavior as well as being a symptom. What I do see is you have them at the bottom of their temperature range. But cooler water is normally better oxygenated than warmer and bacteria do less well the lower the temperature vs the higher. Even so, you may want to bump the temp up a degree or two.
If you have not read these, I suggest you read the piece on keeping botias in general here
http/www.loaches.com/articles/an-introduction-to-keeping-botia and then the piece on Kubotai here
http/www.loaches.com/species-index/botia-kubotai
