I would gladly soak the food as well, but the loaches only eat algae. I can't get them to even
look at prepared foods.

Luckily, the algae sits in the tank for a full day before I replace it (to make sure they get plenty fresh food while the hopefully recover) so it
might be absorbing some of the medicine...
I've been watching them closely and there is nothing unusual about their feces yet. It is the same size and color as I have grown to expect from them, so it might not be flagellates. *crosses fingers* They are still active and eating, so I'm still hoping for a recovery.