tcarter, I agree with you that that could be a problem and is the part that many people (including me) find confusing. As I guess you know, I don't believe in quarantining for many people. It is sometimes called for but in an established system with an aquarist with a few years of experience I believe it is the worst thing for the continued health of fish. (Meredith is cringing her teeth now which is why I generally stay out of these discussions and the reason I wrote a book) In my simple mind, I feel that fish come to us with some degree of immunity. Yes, it is compromised because the fish was off it's food, captured and subjected to all sorts of stress and stuck in a small box for a couple of days so all fish will be harboring parasites and who knows what. That is true. "But" if we take such a fish and then put it in a quarantine tank that is normally a bare tank with some PVC elbows we are further stressing that fish and stress is a big suppressor of a fishes immune system. So there in lies the conundrum. Look up on this, and any other forum how many fish die in quarantine.
Now of course you can't take such a fish and throw it in a tank full of fish that have been quarantined because those quarantined fish have no functioning immune system because they most likely lost their immunity due to first of all their stress while being quarantined, but more importantly because a fishes immune system. like ours will not function for long unless it is meeting those pathogens that it was designed through millions of years to defend itself from. Immunity is a large part of a fishes biology and uses an enormous amount of calories to function, but that immune function is not something we can just turn off and ignore. A fish produces plenty of slime constantly and that slime is there to spread it's antibodies and other immune chemicals over the fishes body. It's immune system is also tied in to it's reproductive system as gut bacteria controls both systems to a large degree which is why live food is an essential part of my theory. It is also why my fish are not only immune, but all of my paired fish are spawning. That is not by accident. An immune fish is much healthier than a fish that depends on you to keep it safe. A fish was designed to live in a soup of invading organisms and it needs those invaders.
To get back to your question. I think when we start a tank we should buy the healthiest fish we can, and put them in a stable, natural, cycled tank and as soon as possible feed them the correct foods. Flakes, pellets and other dry foods will do nothing for a fishes immunity because there is no living bacteria in it. Fish need a constant supply of live bacteria in their gut to stay healthy and yes, to become immune. If my fish can be immune, anyone's can as I am not that smart. Many people say that I am running an ich maintaining tank. That may be true but the ocean that that fish evolved in was also an ich maintaining environment. I am told that if a stress event happens, my fish will die. But my tank has been ich free for 40 years and in that time there have been numerous hurricanes where my power went out for days at a time. Once my tank sitter let the water evaporate to 2/3rds of the tank volume so I couldn't read the salinity as it was off the chart. Once 24 urchins spawned at the same time turning the tank to Half and Half. Another time a very large carpet anemone got stuck in a filter inlet and died and rotted. Nothing ever happened and I still have 25 year old spawning fish.
The correct foods are fresh, frozen or the best, live foods with live bacteria. I feed clams that I buy live and freeze along with live blackworms and sometimes LRS foods which I consider a good source of nutrition and probiotics.
If we are not keeping our fish for at least their normal life span, we have failed. If our fish ever get sick, we have failed. If our paired fish are not spawning, we have failed.
Fish should "never" get sick and most (but of course not all ) fish should constantly spawn because the "normal" condition of a fish is pregnant. If it is not, it is not healthy as healthy female fish produce eggs constantly unlike dogs, cats and most of us.
This hobby is still in the dark ages as far as immunity goes but we are learning and soon our fish will never get sick and we will never have to subject a fish to something that I am sure is a frightful experience such as quarantining.
That is my theory and almost all people on here will disagree with it. I got my experience from spending time with fish underwater and not from the internet.

Meredith, you can start breathing again and I am sorry for throwing a wrench into this discussion. Go about your business