I just went through something similar myself on my 230 reef. From a history perspective the tank was about 2 years ago a fish only live rock setup. It had a fair amount of green algae and elevated phosphates and nitrates. As I got into coral keeping I employed both GFO and Biopellets to pull down those levels. As a FOWLR I NEVER saw cyano, yet N and P levels were high. Over time the tank changed with those levels coming down and I began adding coral. The coral grew well, in particular softies and LPS. I kept up a high maintenance regimen and began to add SPS with success. Being somewhat linear in thinking, I went along with more of what's working is good, and employed an improved biopellet reactor, and continued GFO. My Phosphate levels eventually reached zero, as tested by any of the available hobbyist kits (Red Sea, Salifert, Elos,etc.) Nitrate continued somewhat elevated at 2-4 PPM (based on Lamotte kit as others would indicate zero). I noticed that some softies, like Xenia began to just melt away. Right around this point 3 months ago I had the mother of all Cyano outbreaks. It was well correlated with increased tumble and sloughing off from the pellets caused my constant tinkering in the search for perfection. The output of the pellet reactor does route directly to a large skimmer. The Cyano took me nearly 2 months to eliminate and did not improve until after I discontinued the pellets. I was suffering coral losses, and the Cyano frankly seemed aggressive and where it would get on a coral, in particular Monti's or Stylo's, it would cause polyp death and necrosis. After discontinuing the pellets, I noticed the water was now clearer, and I actually had LESS algae. The glass would stay fully clear for over a week. Cyano began recede. Sadly now my SPS in particular Acros, began to show STN from the base moving up. I figured it must be a low nutrient level given the lack of any algae growth. I began coral feeding and Amino Acid dosing, at lower than recommended levels, and immediately the Cyano came back with a vengance and the STN increased. I stopped all feeding. I finally thought I would try removing the GFO. That left me with no pellets, and no GFO, just a large amount of fresh ROX carbon. Within a week, the Cyano nearly completely receded, the SPS polyp extention increased and the STN stopped and began to reverse on a number of corals. I still can't detect phosphate levels, but now I get a light algae coating on the glass that makes me want to run the magnetic cleaners over the front after 3 - 4 days. Coral growth has now highly resumed on my SPS.
So a very long tale, but I draw, perhaps incorrectly, and clearly empirically, that the type of nutrients and carbon levels in the tank got out of balance. The DOC (carbon) introduced by the biopellets could be used by the bacteria, but not by algae or corals. PO4 became so depleted that corals were starving, while at the same time the bacteria load in the tank went very high and became pathologic . Another odd observation is that a 12 year old Passer angel in the tank began to show HLLE during this period, which reverted after discontinuing the pellets / GFO and just running fresh carbon. I again attribute this to excessive bacteria levels in the water.
My recommendation is that we need to be careful as we drive to ULNS systems, that we need to keep those low levels in careful balance. Unfortunately I don't believe we have all the tests available to us, as we can measure N & P to some degree, but other nutrient levels from sources like biopellets can not be tested with hobbyist grade tests. I also think that truly ultra low levels of P can be taking things too far.....