Yes, and by offline, I do mean your bucket. That is a pretty tight loop, so water would still be O2 starved even with your koralia. And the presence of all that mulm/muck build-up could be trapped or dying carbon and nitrate laden bacteria, that isn't being flushed out into your skimmer.
And after you put it back online with your tank, the mulm/muck probably continued to build inside your reactor because your outlet was partially plugged.
I may have missed it in all your posts. But does your reactor effluent go directly to your skimmer input?
Despite all that, I am not saying either that was the direct cause of your current problems with your SPS dying. But it may have started the ball rolling, and caused other things to get out of whack. If your ammonia is high, though, sure does seem like a mini crash happening...
Again, I would do massive water changes. And keep that bio pellet reactor offline until everything stabilizes. Then you can start again with getting your nutrients under control, but this time, do things slowly and gradually, and watch your tank and corals closely to see how they are reacting.
If you look at the beginning of my tank journal, I started with a 100 ppm nitrate tank, with very high phosphates (after inheriting a 10 year running tank). It took me a year or more before I finally got everything under control. But has been running clean (zero nitrates and near zero phosphates) for a couple years now, and growing SPS like crazy.
I know your tank was looking great with all your SPS before, too. So with a bit of patience, I am sure you can do it again.
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