What type of flatworm problem do you have? Beyond smothering your corals, I've read that the common red planeria is no real threat.
I had a small break out of flat worms but it took care of itself with more diligent tank housekeeping. It seems that the 'fix' to these types of common problems are the same thing - reduce phosphates and excess nutrients. Supposedly every aquarium has flatworms, but they are only noticeable during a break out.
Have you tried increasing your skimming, water changes, flow, and less food at feeding time?
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