You've touched a very important part of the treatment process: proper diagnosis. "It goes away and then comes back with a vengeance" is not what true Marine Ich (
Cryptocaryon irritans) does in real life while being treated. BUT there can be two explanations for what you see.
The part of the cycle which is very susceptible to hyposalinity is the 'encystment' stage (known as Tomonts) and the free-swimming infecting stage (known as Theronts). If you see white spots on the fish, then the parasite is ahead of (just before) these two stages. If you see the fish clean, then the parasite has moved on from this stage OR Theronts that were already on/in the fish which you haven't seen are there, engorging themselves but not yet invisible.
So the ones you now see, after the first group seem to have gone away, are either the ones that lived through the hyposalinity exposed Tomont and Theront stage and now back on the fish OR are actually more Theronts that were imbedded in your fish as Trophonts, that just weren't visible. Does this make sense?
Too often people think it's gone then comes back, when there is another explanation -- the Trophonts were there on the fish, just weren't visible yet. The only part of the cycle we humans can see with the naked eye is the part after the Theronts have attached, they have become Trophonts on/in the fish, and now are engorged or 'pregnant' and ready to go on to the next stage. You might call these the 'mature phase' of the Trophont stage. That's what we can see.
So let's look at the two possibles: Did the parasite go all the way through the vulnerable stages to return to infecting your fish or were they already there but not yet seen? For the former, you would have to come up with a scientific reason why they weren't killed by hyposalinity when the world 'knows' (?) that hyposalinity kills them. For the second possible, all you need do is acknowledge that they were there, but not yet visible to you.
There is a scientific explanation of the former case. Dr. Burgess refers to the hyposalinity treatment as a 'stressing of the parasite' and not an outright killer. Thus, some would squeak through the process on one or two rounds, according to him.
Remember the parasite is in all different stages all the time. They move from stage to stage in a time range and thus they are not all in sync with each other. So the second possible now gets the majority support of what is happening.
What can happen, from my experience, is that a very small number (small percentage) of Tomonts and Theronts squeak by the first hypo effect. They were 'hurt' and 'stressed' but not killed outright. That is one reason I favor the salinity of 11ppt -- lower than 1.009 sp. gr. In essence, any higher salinity does allow a small percentage to 'squeak through.' But this percentage is low. What
usually happens is that the Theronts were there on/in the fish, but the aquarist just couldn't see them yet until they entered the 'mature phase' of the that particular stage.
Now to your questions. . .
1) Yes. The hypo treatment doesn't alter the time of parasite's stage on/in the fish. Yes. In fact this is the
only time the fish is stressed. Humans really don't know, but it could be like you were being stung by a mosquito constantly, but unable to get it off of you. It can drive the fish mad, as such a mosquito would do to some humans. People who take no action to help their fish get rid of this infection -- who let the fish 'fend for itself' -- are, in my opinion, torturing their fish.
2) Although possible, I'd say not likely. The swing upward would need to slip it to the 14ppt salinity level. I think more likely you are just seeing the 'mature stage' of the Trophonts that were already there, but invisible to you OR a very small percentage of those that made it through the hypo treatment (all of which is detailed above).
Brooklynella is a disease caused by a different organism -- a protozoan to be exact. This organism has no free-swimming phase and just lives on the fish. It eats the fish, so to speak. Usually it starts with the gills and goes on to surface tissue and blood cells. There are a considerable number of scientists who believe that Brooklynella infects fish that are stressed and that theoretically the fish can fend it off naturally if they aren't stressed. I have no firsthand knowledge.
But, what captured fish, held prisoner in our aquarium is not stressed? Prevention is far better than trying to do a cure later on. A fish with Marine Ich exposed to Brooklynella would, in essence not stand a chance to fend off the Brooklynella.
