I think at least in your titular question, you're mangling terms in a way that is unhelpful.
In logic and critical thinking, valid refers to when a deductive argument is such that if all of its premises are true, then its conclusion must be true (there are other similar but more exotic formulations -- e.g. must be constructable as a model -- but those don't change the point here).
Fallacy is term with two meanings that are both "errors of reasoning." Deductive fallacies are known forms where an argument is presented as deductive but is not valid. For instance,
"affirming the consequent" = If A, then B. B. Therefore, A.
Such errors are damning to any argument that presents itself in that way.
"fallacy" has a second meaning which refers to bad reasoning in an informal sense. "appeal to ignorance" is an informal fallacy of this short.
"Fallacy" as used in the latter sense doesn't automatically decide whether someone has committed an error that destroys the argument. Instead, it often devolves into an argument about whether the claim in question is fallacious to use in that context -- since it is not definitely an error in formal reasoning.
For instance, "ad hominem" is an informal fallacy, but "you shouldn't trust him, because he's lied to you 100s of times" is not guilty of an "ad hominen" attack on his character, it's good reasoning as to why you should not trust him. (whereas "you shouldn't trust him, because he has brown eyes" is fallacious and ad hominem).
Given this, it's unsurprising that one can find an argument which appears to use the fallacy and prove something correctly. This doesn't disprove that it's possibility to fallaciously confuse absence of evidence with evidence of absence. It merely proves that the fallacy is informal. And in all likelihood proves that when applied to a controversial case that people will find grounds for disagreement.