Hope your treatment continues to go well! I had brown flatworms in my biocube 32, not nearly the population you seem to have had. I used FWE, followed the directions, did a large water change an hour later etc etc. I lost a midas blenny a couple days after the treatment. Everything else did fine. It makes me wonder if there was something else going on with the blenny that I didn't recognize, and the flatworm toxin was a final straw.
I still have a few flatworms. I have a pink streaked wrasse in quarantine to try to combat them. I would have gotten a yellow wrasse if the tank were big enough.