Hi Erik! I'm writting you beacuse I have some koi with a few red and clamped fins. I'm thinking about costia or trichodina but I dont have acces to a microscope to check it. I recently check my water parameters and are good. I'm from Spain and here It's springtime.
My pond its located near a forest and sometimes frogs came in so I supose maybe the parasites could came from that.
If you treat the pond with Formalin according to label instructions once a day x 4 days then skip a day, treat again, and skip a day and treat a sixth time – it's unlikely that you will destroy MUCH of your beneficial bacteria.
If you perform a partial water change after each Formalin application it's even LESS likely that you'll do much harm to the beneficials.
It's mainly a “big deal” if the fish are crowded and the filtration / biological filtration is already strained.
If it's springtime, I suspect that the water will be cool enough for safe use of Formalin Malachite Green.
Let me know how it goes.