I never had a problem with the Flatworm Exit, and I didnt adhere to the whole 25% water change idea either.  My skimmer collected almost all of the 'juice'.
Of course, every system is different... yours might not be so lucky to handle the byproducts.  I use refugiums, phosban, carbon, a good skimmer... as well as the 'vodka' method to reduce phosphates and nitrates.
Hmmm.... that gives me an idea...
Perhaps you might want to add some biological filtration (wet dry/fluidized bed/ bio-balls).  This will provide a medium for any ammonia and nitrite to be quickly converted to nitrates.  Then, get the vodka method going (about 2 shot-glasses of everclear every day will do it for your system)... this will enable the bacteria that feed on the sugars in ethanol to build up.  These bacteria feed on phosphates and nitrates in the process...
Then, use flatworm exit... being sure to remove carbon during treatment and make sure your skimmer is ready to go (freshly cleaned).  Also, I usually do about 2x the dosage compared to normal...  these red buggers seem extra hardy.
Then, after a day, put the carbon back in use, check the skimmer (you should have collected nothing but red crap all night), and continue the vodka method.  
The extra bio-filtration will of course boost phosphates and nitrates, but it will process ammonia and nitrites.  Normally, this would be a bad thing, but the vodka method makes the bacteria bloom to digest the nitrates and phosphates.  Then, these bacteria are collected in the protein skimmer, nutrients and all.
This may be the little 'boost' you need to handle the mass die-off.
Regards,
Jon