Hi Sam,
I only treated the corals that were affected. I spend a lot of time looking at my corals, and can usually see if one is 'not right'. After the original incident that spawned this thread, I didn't see any for a year. Then on a totally new A. valida frag, I noticed a bunch of bite marks and even eggs.
With that amount of eggs, it was easier to throw away the center of the coral. I kept the base that was fine, and the tip that was AEFW-free.
The base has been growing quietly in my reef ever since. It really doesn't have much to show for itself after all this time, but it is alive.
The tip ended up getting reinfested in a totally different spot. Because of its location, I can't see bite marks, but the coral is faded with little color. What I do is every two or three days, I blow off the usual suspects with a turkey baster, sending any flatworms flying. My fish are eating them that way. I added a tiny Yellow Coris Wrasse that fits into the nooks of my SPS to help work on these pests.
Am I out of the woods yet? No. Every new addition is carefully dipped and studied to make sure nothing new sneaks in. I've been doing so for the past couple of years since the original outbreak, as I don't want to add to the current problem with even more of these suckers.
The reason why I've never set up a 6 week quarantining process is because you have to set up an entire reef next to your actual reef. All the SPS are moved, all are treated, all are handled, and all are stressed. You have a new tank with new flow patterns, different lighting, and a bunch of upset corals. All those stressors are in place, and the corals usually don't handle a lot of stress well.
Worst case scenario - they eat the corals and I simply can't keep those in my tank any longer. Since they have a certain type they like, it would mean I'd have to give up keeping those particular ones. Fortunately, that hasn't been a problem.