Thanks. All good questions. I probably don't know at least as much as I know, but here's the order of events:
Began upgrading from a 200G tank that was having glass issues to a Red Sea S1000 (so new tank, sump, but existing hardware).
Used a local aquarium service to do the transfer. He set up a very makeshift temp holding tank with it's own sump and put in all rock, corals and 11 fish.
He did forget to put in the heater, but I discovered that within a few hours.
The fish seemed to survive well in the temp tank setup, although some of the more sensitive corals were already showing signs of tissue loss (lighting change?)..
Day 1: it took him about a week to come back and move in the new tank, fill it with the rock and water from the temp tank, and he also rinsed the sand in clean saltwater and reused some of it (I was not a big fan of this but he assured me it would be ok. He also added new Arag-alive sand).
He had broken the skimmer and left about 40 biomedia cubes in a dry bucket (I know, it gets worse) so part of my bio filter was gone (I've since replaced the skimmer) - Nitrates peaked at 39.5 and phosphate at 0.35 before they started coming down.
I have a separate QT - in a moment of weakness a week or two before I had bought a mimic tang at my LFS which died within a couple of days so the tank had been empty for over a week.
while setting up new tanks, he ran out of newly mixed saltwater to top up the new larger tank and unfortunately took 5G of the old water from the QT and put it into the new tank (told you it got worse).
He then put the fish and corals into the new tank.
Day 3: A couple of days after the new tank was up and running one of the pyramid butterflies started hiding and getting listless - developed what looked like popeye in one eye. Thought it may be wound-related following the tank transfer.
Day 6: First Pyramid butterfly died.
Day 15 : Second pyramid began showing signs of cloudy eyes (both eyes)
Day 16: Began dosing KanaPlex in DT after Copperband also began showing slight cloudiness in eyes.
Day 17: Second Pyramid died. Copperband showing signs of infection on flanks.
Day 18: Copperband died. Second dose of KanaPlex. Watanabe Angel died over night - difficult to see what the cause was as a large Sallylightfoot crab was making a meal of her. Interestingly, the Sallylightfoot also died a couple of days later.
Day 19: Both Swallowtail Angelfish and both Clownfish died (pictures posted above)
Day 20: Foxface and Gem Tang remain, Foxface stopped eating for a day but ate an hour ago. Gem Tang seems fine so far. Final KanaPlex dose due tonight.
The corals I believe may have died from the stress of the tank transfers - it seemed to be the Acros and Montis and a large Stylo and Favia that got hit, the Duncans and GSP survived - go figure..
Other than the spike in nitrates other parameters have stayed pretty stable - pH, temp, salinity. Alkalinty did drop a little in the temp tank but is now back around 9.