I wouldn't consider metro to be effective at eliminating all protozoa. It is certainly effective against luminal (internal) protozoa. Efficacy against ectoparasites (Brooklynella, Cryptocaryon etc.) appears to be hit or miss. Likely there is something about the pharmacological action of metro that is not effective against Cryptocaryon.
Personally, I would not use metro for Brooklynella. Formalin is a much more effective treatment.
I was treating based on this, am I misunderstanding something:
Prescription Medicines
Flagyl (metronidazole) is by far the most effective drug available against these diseases. Indeed it is the only effective treatment for fish that are internally infected with Uronema marinum, but it has to be administered in the diet. To treat with Flagyl (metronidazole), add 34mg/l (34mg/kg bodyweight is required if treating the internal disease) of the drug to the aquarium water to be treated. A single dose should be effective, but it can be repeated daily, if required, as the drug is well tolerated by most fish. It is a very reef safe drug having little impact on invertebrates BUT it will kill off all protozoans and anaerobic bacteria in the treated tank, so, like all medications that are used in a reef tank, it will have some undesired effects on the ecological stability of the tank.