First, I'll say good luck. I've been battling flatworms for months, so I'm tagging along. I'll give you my experience and what I've learned researching.
Flatworm eXit in itself won't harm anything but the flatworms. However, when the flatworms die they release toxins, and that's what can cause your tank to have serious health issues for your corals and your fish.
Get a long piece of regular airline and a media bag. Tie the bag around the airline and place it in your sump. Take the other end of the airline and hold it against a powerhead until you get a siphon started. Now, start sucking the little buggers out. They come offf the rocks and corals quite easily, flow down the airline and get captured into the media bag. It's almost enjoyable, actually. Suck up as many as you can. Wait a day, do it again, etc etc. Until you can't see anymore that you can reach.
Once you've done that, start treatments with the flatworm eXit. Follow the instructions, especially the part about having fresh activated carbon ready to go. The Carbon will help to remove the toxins being released and help to protect your inhabitants.
Now, for my story. I've done this so many times I can't count them anymore. You don't even want to know how many bottles of eXit I've gone through. The worms die when I put in the eXit (I actually dose 2x the recommended dose) and it sure does appear that they ALL die. They, however, keep coming back and I cannot explain it.
I can say that after at least 7 or 8 treatments that I've done, I have not lost a single invert, coral or fish. I do notice that my pod population has significantly diminished, however.
So, After seeing what I've seen, I can attest that the flatworm eXit does in fact work very well, but that the little buggers are stubborn as all get out. The less of them you have in the tank when you dose, by siphoning them out first, the lower your risk is.