OK I am going to stick my foot in it here by going against the norm, but have have had quite a bit of experience with Clown Loaches. I have lost them using DIY CO2 in my 340 gallon planted tank. You can lose them in a 125 Gallon tank with DIY CO2.
In your case however I am not sure why you believe they are at risk, other than that one died, which happens sometimes. If it is just because they are hiding, well, that happens sometimes also.
I do believe that you are cleaning your filters too often. That could really mess with your biological filter. The things I'd check are ammonia, nitrite, and nitrate in that order (which may be obvious). If anything is out of line there I would do a 30% water change right away and daily till the parameters come back in. Other wise I would go with 25% weekly water changes.
While I agree that the way you are doing CO2 is probably not a concern, you can't rule it out. If you have any fish gasping at the top of tank, pull your CO2 and do some more research. I keep my water around 81 degrees. If you are concerned about them hiding, get some dither fish. Good luck, and if you find that they do survive get a couple more. I presently have 6 in my 340 along with a couple zebra loaches to keep them motivated. They are the showmen of my tank.