Figured I'd give a bit of an update on my use of this method.
I started using hydrogen peroxide last Monday (10 days ago). I determined that I needed to dose 11 ml each night for my total system volume. I would dose at about 9 pm each night and left my carbon reactor (added new carbon prior to dosing) and protein skimmer running. I dosed for 7 nights as I had a very large population evident in my tank. On night 8, I replaced the filter sock, cleaned the skimmer and let the tank "rest". Night 9, with a much lower population evident, I dosed 65 drops of flatworm exit and watched the tank over the next 5ish hours. Yesterday was another "rest" day, and this evening I have dosed 100 total drops of flatworm exit. I will base my next plan of attack when I get a good look at my tank tomorrow.
A few notes: I feel like the hydrogen peroxide was an ingenious find and a very useful tool. The use of it before dosing flatworm exit, I feel, has mitigated the concerns with the use of flatworm exit. I did notice that my corals reacted to the first dosing of FE, but haven't reacted the same way today.
I only have a 6 line wrasse in my system as far as fish go. 1 coral banded shrimp, 1 emerald crab, trochus, 1 Mexican turbo, and assorted hermits in the tank currently. I noticed no ill affects to any thus far.
Hope this helps anyone considering using this.