I bought some fish, who's fins looked like they were melted together, (it was nothing I did, they came with it), and I dosed the tank with Melafix, and they are perfectly fine now. Melafix and Pimafix will not mess up your biological filter, no worries there.
Also, I used the meds with my loaches in the tank, which are also scaleless, and they were fine. Believe me, I research the stuff before I it in the tank, and those meds are fine for scaleless fish.