Knowing what went wrong is the first step in dealing with it. If it was a toxin in the tank, or a water quality issue, then sterilizing the tank is not required. You will want to remove any toxin, for example running a few cups of activated carbon in the filter will remove many possible toxins, especially combined with several large water changes.
One possible idea: Loaches are more sensitive than many other fish about oxygen levels in the tank. Could the O2 level have dropped, perhaps due to poor water circulation or some other cause?
If you are still sure that there is a disease or parasite at the bottom of this, and want to kill whatever it is,and be sure it cannot come back here are a few ideas.
To sterilize a tank, just in case something is lingering you need to sterilize and
not re-contaminate. The way you want to alternate cleaning the filters is NOT a way to sterilize the tank. Whatever is in there will move right back into the first sterilized filter and live there when you remove the other filter for treatment.
If you want to sterilize everything here are some basics:
1) Remove fish to as many tanks as needed:
Depending on the treatment you are planning some fish may not handle one certain medication, but are tolerant of another. So, separate the fish according to which treatment they will handle. You are likely going to use medication that would kill any nitrifying bacteria, so plan on doing enough water changes to keep the ammonia as close to 0 ppm as possible. Do not put too many fish in any one tank. Perhaps 5" of small fish in a 10 gallon, and even then the ammonia will build up fast. Medicate with at least 3 rounds each of two different parasite medications, and 2 rounds of antibiotics. Levamisole is a good parasite med, but will not kill all parasites, so do another round of treatments with something else.
Kanamycin is an actual antibiotic, meaning it really kills bacteria. If you can get or make antibiotic food this is the best way to treat. Compare to Melafix and Pimafix that simply slow the growth of bacteria and fungi that may be on the outside of the fish.
2) Throw away plants. There is no sure way of sterilizing them without killing them. If half measures are OK, (meaning whatever disease might survive) then treat the plants with potassium permanganate OR bleach and then grow them in a separate tank with no fish for at least a month. This may break the cycle of whatever parasites or disease might be lingering. Without a host, most parasites or diseases will not survive.
3) Remove and sterilize all equipment. Throw away filter media. There are too many holes and places that may not get properly treated to risk saving it. You could try boiling it, but this will kill the nitrifying bacteria anyway, so I would just start with all new media. Lava rock, and similar material is also a poor risk, though you can heat it to kill microorganisms (boil or bake lava rock). You sure cannot keep nitrifying bacteria alive while killing other bacteria or parasites.
4) Remove and sterilize all substrate, decorative rocks, driftwood and so on. Depending on treatment some of these things may not be worth saving. Heat treatment is probably better for driftwood and substrate.
5) Reassemble it all, using Dr Tim's One and Only or Tetra Safe Start to recolonize the filters.
Materials and methods to sterilize all these things:
DO MORE RESEARCH BEFORE TRYING ANY OF THESE.
WEAR GLOVES AND EYE PROTECTION.
If you knew what disease or parasite you are dealing with then these suggestions would be specific to that problem. However...
Strong salt solution: Will kill many parasites, and will rinse clean very easily. The tiny remnant if it is not well cleaned will not hurt the fish. Warm some water on the stove and stir in as much salt (sodium chloride) as the water will hold. Allow the water to cool until it is comfortable to touch. (75*F to 90*F is safe for all the stuff in the aquarium) then soak everything, and wash the tank out several times. If this is an acrylic tank be very sure the salt is fully dissolved. If it is a glass tank then you can actually use dry salt as an abrasive to scrub the glass clean, while washing it with very salty water.
Bleach: Will kill all sorts of bacteria. 20 parts water: 1 part bleach is safe for some very durable plants for a 30 second dip, and have a bucket with double dose of dechlor ready to rinse them in. Aquarium equipment can be cleaned with a stronger solution, and lots of rinsing, followed by a soak-rinse-soak in water with a double dose of dechlor. If you can still smell chlorine the repeat soaking and rinsing with more dechlorinator in the water. Will not kill mycobacteriosis.
Rubbing Alcohol: Will kill mycobacteriosis. I think 70% is the one available in the USA. Do not dilute it. Removing it from the tank and equipment might be a bit of a problem. Try rinsing well, then exposing it to the sun to evaporate whatever rubbing alcohol is left.
Potassium permanganate: do more research! It reacts with organic matter so clean the gravel or sand really well before using this, then rinse REALLY well. Hydrogen peroxide will deactivate the potassium permanganate, then you still need to rinse the stuff away.
Hydrogen peroxide is one of the safer ones in case there is a little tiny bit left after rinsing. Sunlight will break down the H2O2.
Other liquid disinfectants and similar treatments: I am leery about using these on a porous material like driftwood. The driftwood might soak up the stuff, then release it into the tank. Salt water soak might be OK, especially if you then soak the wood in several changes of water after.
Heat: Driftwood can be baked in the oven. Put it in wet. As it bakes the water turns to steam and kills all sorts of things. Bake it until it is dry. You will then need to boil it to make it soak up water, or at least soak it for quite a while. Most other aquarium things will not handle heat, for example plastic plants are not likely to survive a dishwasher when the heated dry comes on.
Gravel or sand could be boiled or baked, but do this outside, such as on a bar-b-que. You do not want the smell in the house.
There is another way to heat treat things. It is called solarization. It means to use solar energy to heat the material. Think of a car on a hot day. You will need to build a box with a glass lid big enough for whatever you want to treat. Put the object(s) in the box while they are wet and close the lid. If the sun shines directly into the box all day it can get hot enough to cook in there, and the steam generated will kill a lot of things. The better insulated the box is the better it works. Mildly warm is not going to do the job. If you opened the box and could still touch the stuff inside this is not hot enough. This is a good way to handle the substrate. I learned about this method to treat soil used for starting vegetable seeds.
Just in case you want to investigate mycobacteriosis here are a couple of links. This problem does not sound like it, though. Mycobacteriosis in more often a slow killer, or hiding in the background weakening the fish which often die of something else that they were too weak to fight off. It is odd that you had so many deaths all at one time, and limited to Loaches. Sounds more like a disease or a toxin in the tank.
http://www.aquaticplantcentral.com/foru ... -fish.html
http://edis.ifas.ufl.edu/VM05538 tanks, 2 ponds over 4000 liters of water to keep clean and fresh.
Happy fish keeping!
