Well I guess its a good time to update on where the tank is at right now long post warning
To start with I haven't tried adding any more stony coral since July, however since then the rest of my zoas kept dying off, first every zoa on the right hand rock and then all the zoas on the left hand rock, it was really weird that they didn't both go at the same time, especially since both rocks had the same kind of zoas on them.
Then around the time all the zoas were gone my mushrooms and rics started bailing out. One by one. They would all start to ball up and then let go. Some were fairly new but most of them had been happy where they were for almost a year. I still have a couple left over that haven't yet bailed but they don't look too far off, a couple floated to low flow areas and found somewhere to reattach for now but most just disappeared/floated to low flow areas to die.
All 3 clams, 2 BTA and both leather corals are still alive. The leathers will occasionally look a little ticked off but most days look OK and the clams and BTA are still thriving and growing (I don't know if I could stop those NT aqua cultured clams even if I wanted to

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So far the weirdest thing I have noticed is whatever this is only effects one kind of coral at a time. First stony corals, then zoas, then mushrooms and now maybe leathers. To me that points to a fish picking at them but I have been keeping an eye out for it and haven't noticed any, especially since I only have 2 fish now I would have thought it would be easier to notice.
Around mid July all my fish except my Blue tang and Black cardinal died within a week from velvet. In Australia we cant get CP and copper would have taken at least a week to get to me so I just assumed the 2 survivors wouldn't last that long. To top it off from July all the way until the end of September was hectically busy for me including a month away so I kind of just let the tank do it's own thing, the only thing I did to the tank is empty the skimmer and dose vibrant once a week, I didn't even feed the surviving fish :/
To my surprise the vibrant worked, I'm not a fan of using unknown chemicals, especially something I considered to likely be snake oil but it worked, major results within 4 weeks too. I don't know if it will come back if I stop dosing but all the derbesia algae appears to be gone. I finished one small bottle and started on a big one. I'm going to finish off the big bottle and stop dosing it to see if the algae comes back. I might order another small bottle to keep on hand in case it does come back so I can stop it in its tracks. Was the algae releasing something into the water? No idea, a few mushrooms still bailed after the algae died, and the remaining ones haven't been looking better but they are still there for now. I also can't say for sure if it was the vibrant or not (pretty sure it was though) but the cheato in my algae reactor died. I replaced it twice and both times it died off again and I just couldn't get it to grow.
As another surprise to me the blue tang and black cardinal are also still alive and well. No spots of ich or any signs of velvet (apart from the tang swimming into a power head once in a while), when I got back from my trip and realized they weren't going to succumb to velvet I started feeding them again and they are looking fine.
The plan was to pull them out and treat them while the tank goes fallow. However after doing some reading (in particular a thread by Gweeds1980) I am going to give the Paul B method a go first. I am going to try and encourage the natural immunity that these two fish appear to have to ich and velvet and see if I can run an "immune" tank. This is a big maybe and could very well fail, but worst case scenario I have to go back to my original plan and treat in QT while the DT goes fallow, no big deal.
Part of going down this path of an "immune" tank is doing a bit of a tank reboot most of which I was planning on doing anyway while the tank was fallow. As a part of the reboot I will be doing the following:
1) Redesigning the sump. Removing the filter sock section and adding in a refugium section before the skimmer. The fuge will be as large as I can make it and lit with an LED grow light.
2) Stop using ASW and go back to using NSW. This is going to be a pain in the a** as collecting NSW for a 4' tank was hard enough but that extra 2' means collecting a massive amount of water

I am still undecided as to how I will do this one.
3) Remove that dang sunken ship. The ship was a compromise with the wife and I thought the Triton test might show that it was causing issues but it didn't show anything definite. However I still think there is a chance it could be a cause / contributor of my issues so the HMAS Compromise is going.
4) Remove the black sand. I loved the black sand when it first went in, it really does make coral colours pop like crazy. But I just can't stand how dirty it gets and where it isn't dirty it's growing coraline algae like crazy! I now have purple sand in most places and I have to constantly turn it over to stop the coraline. While I doubt it, the black sand also could be a possible contributor to my issues. I will be running BB while all these changes settle in and I will get some good proven white calgrit at a later stage if I ever get some fish that need sand.
5) Stop dosing Vibrant. I don't know how this well this will go but once I get the fuge done and some cheato and some caulerpa in I will stop the Vibrant and see if the macro + skimmer can stop the algae from coming back. I will also be getting a re-vamped CUC from the local wholesaler, he's got some awesome short spined urchins and some little hermit crabs that he says stay tiny and will eat any kind of algae you might have.
6) Start feeding a bit heavier with fresh DIY fish food full of bacteria. I will be getting whole fish, squid, muscles and fish guts and blending it all up with wild caught shrimp & crabs as well as frozen mysis and black worms (if I can find them). This food can apparently help fish with their immune systems and I have no doubt it will be good for coral.
I am hoping to get all of that done over the next 2-3 weeks and then on the 3rd of Jan I am going to go out at low tide and get a couple of small "tester" pieces of coral to see how they go in the tank. Fingers crossed!
Also I would rather keep this thread at least semi on topic of coral issues so please avoid comments about QT vs disease management tanks as I know many people have very passionate views on this topic and there are many other threads where this can be discussed
Cheers,
Macca