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It is unlikely that they stayed on the fish the entire time. Fish can build an immunity to marine Ich. The trophonts cannot feed as effectively and reproduce in much lower numbers but they still follow the same 3 to 7 day time line. Keep in mind that you don't actually see the Ich parasite on the fish, what you are seeing is the mucus excretion on the site where the parasite is. If the parasite isn't feeding effectively, there is no visible excretion on the outside of the fish.
The downside is that if the fish experiences a stressor that weakens its immune system it will start showing symptoms again.
From the University of Florida (great article covering Cryptocaryon)
Fish that survive a Cryptocaryon infection develop immunity, which can prevent significant disease for up to 6 months (Burgess 1992; Burgess and Matthews 1995). However, these survivors may act as carriers and provide a reservoir for future outbreaks (Colorni and Burgess 1997).