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What how much Flatworm Exit did you use?
Were you doing the recommended per bottle or per a lot of the reefing community has used?
I find that per bottle directions will not effectively kill them. Depending on your concentration of flatworms, they will still survive even at 1.5-2 times as recommended by other reefers.
I've had them twice once in my old tank and once in a frag tank. I've dosed at 2-3 times the indicated dose and repeated the dose a week later just to make sure all were killed and it worked fine. Weeks before treating I siphoned many of them to decrease their numbers and the toxins released when they die.
I now religiously quarantine and dip all my corals and make sure to avoid them in my system as the worst part is that they don't cause any damage to notice the so you only realize you have them when their population explodes.
You can do a follow up dose if desired.
Watch the tank closely and observe the sump
This is commonlooks like after the first dose it's not knocking them out cause this morning I could still see some stuck on the glass and they appear to be moving around in a normal fashion. should I increase the dose tonight? how much?
This is common
I doubt increasing the dose will help.
Take a look here for a good method against flatworm
https://www.reef2reef.com/threads/peroxide-and-the-use-against-flatworm.228032/
Don't know which one we are talking about so here is for both methods
You can continue to dose FWE but I don't know what the effect of long term use is.
Long term dosing of h2o2 has been well documented to not interrupt the tank
From my own tests it took about 3 days on the average although my populations were not as large as I had to grow them to test.correct, I was referring to your method; H2o2
I was under the wrong assumption you should only dose h2O2 for a certain amount of time(days). So the concept is over a couple of weeks you're slowly whittling down the population of flatworms via mechanical filtration until they are all gone. based on your experience how many weeks does it typically take? are we talking weeks or a month or two?

