Precisely. How could He? Yet the reality is that this is a genuine miracle occurring in the context of all that. Do not miracles draw souls to the truth?
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The blood of St. Januarius is the blood of a truly Catholic bishop, of a saint and martyr. The miracle of his blood is a (apparently) permanent institution that God appears to will to continue indefinitely, maybe until the end of the world. It vindicates St. Januarius and his sanctity and martyrdom, not the person holding the glass vial of his blood. Just because heretics have obtained possession of his blood doesn't mean they are vindicated when it liquefies.
You might as well claim that if heretics obtain the possession of an incorrupt body of a saint, that the body would have to immediately begin to decay when they get the keys to the church. Or that a eucharistic miracle on display, such as a host that turned to flesh, would have to turn back into the appearance of bread if heretics get possession of it. None of this follows. Those miracles represent, respectively, the sanctity of the saint and the blessed sacrament, not the person possessing them.
you have to come up with an explanation as to how there can be still so many genuine miracles that are not in traditional chapels, but in the churches that are in the possession of the innovators.
No, there aren't. The people who vouch for the authenticity of these things have no credibility.