Saying that "we thought X was dangerous, we looked at it closely and it turns out X isn't dangerous at all" has the same meaning as "we mis-estimated the danger from X and then corrected the estimate".

Risks and dangers here are percieved risks and dangers. In that context, such talk makes sense - obviously percieved risks depend on your current state of knowledge. Maybe god knows whether the bad thing will happen or not - but without a hotline to Him, percieved risks and dangers will remain the best we have.