Age old dilema... Can/should I run a skimmer with scrubber?

I don't think it makes a ton of difference which comes first for the majority of cases. There are some instances where a scrubber is placed after the skimmer on a relatively clean tank, and it has trouble getting started. My thought on that type of situation is that the screen is over-lit, either too intense or too long, or both, and this causes photosaturation and prevents growth from getting a foothold. But once you have established growth, I think this concern goes away because both a scrubber and a skimmer are not single-pass devices - the effluent from either is not 100% filtered on each pass, so there is plenty to pass on down the line.

There are arguments for putting either the scrubber or the skimmer first. IMO the main arguments are scrubber first gives it first crack at the tank water, skimmer first means you can feed the scrubber a mixture of tank water and skimmer effluent which is highly aerated, which can benefit scrubber growth as well (lots of O2 and CO2 infused into the water exiting the skimmer). To a certain extent, scrubber then skimmer will still provide the scrubber with aerated water as it returns back from tank to sump, but undoubtedly less "rich"

As for your situation with the calcium reactor, that's a bad situation. Calcium reactors can be finicky and the needle valve is one piece of equipment that it notorious for this. If there is one part of the reactor that you want to be top quality, that's the part. Once you have that taken care of, they can be very effective. Dumping the contents of the reactor into the tank all at once will drop your pH so far down that it can very easily kill off everything in your tank, corals, fish, bacteria, etc. If that didn't happen, you can bet that there was at least a bacterial colony crash which means lots of nutrients suddenly became available, and if it dropped down below 7.0, then you probably had some de-crystallization of the live rock. What I mean is that calcium and phosphate chemically bind in higher (normal) pH and deposit onto the rock, and when the pH drops down below 7.0, this can reverse, dumping phosphate into the system. In the "phosphate flow" scenario, which purportedly causes lengthy algae blooms on the rock after adding a scrubber or dropping the phosphate down after a long run of high phosphate, this is likely to be done by phosphate solublizing bacteria (PSBs) which takes a long time. In your situation, you may have released a good amount of this and the cyano, being one of the oldest forms of life on earth, has jumped on the situation. I've seen cyano outbreaks occur similarly when the Alk spikes way up - similar reason, a bacterial colony crashes or is thrown out of stability.

So really it's a matter of re-stabilizing the system and then keeping it there. The cyano should "burn out" but it's going to keep going as long as it has fuel, so it really becomes a game of waiting it out and keeping it at bay. What you really need to do it just hit it at all angles until you start winning the battle. My suggestion is to use carbon and/or purigen, skimmer, scrubber, and then reduce your feedings to a minimal amount, feed 15-20 minutes before lights-out, and maybe go to every other day feeding.

Some recommend a 3 days lights-out and total blackout period (wrapping tank in blanket, 0% light in the tank), and you can try that but IMO that's a last-ditch solution, and really doesn't "solve" the issue permanently. But if you have corals that are losing the battle, total blackout will not permanently harm them, and when the lights are back on, they will be able to recover without the cyano damaging them. The cyano may come back, but if you keep up on your filtration media changes and siphon out any cyano that starts to pop up, you can likely avoid needing another blackout. For the siphoning out, I would use a section of hard airline tubing with flex airline tubing connected to it, this lets you siphon out a very small amount of water while getting a lot of the cyano - typically you only siphon out about a gallon in 15-20 minutes if you pinch off the tubing when you are not targeting cyano. I use this technique for dinoflaggelate outbreaks.

If you scrubber screen is very mature, you might want to try jumping the hours up to a very long daily photoperiod, as long as it can handle. you can even go 24/7 as long as you don't bottom out nutrients to the point where the screen turns white. I've been running my L2 lights 24/7 for a few months now (after accidentally leaving the timer outlet switch in the "on" position) and it grows great - but I'm feeding heavy and I don't have the situation you have. Doing that now on your tank under a restricted feeding situation might not work the same. So I would consider extending the photoperiod, but you probably want to test nitrates and phosphates first to see if they are elevated (meaning, food for the scrubber)

 

I don't think it matters much on order, for any of those.