I mean, the plaque might still have an effect; it's possible that exposure to the viruses described in the article could lead to higher levels of amyloid beta plaque, or cause the plaque to be more harmful. Kinda like how a broken leg might be caused by a fall, but the actual problem wasn't the fall, it's the fact your leg is broken.
Except the original study wasn't properly vetted for decades and it really set us back because we blindly followed the wrong path. Science institutions failed this time around. In this case, the money was more of a tragic loss.