I pulled up the carpet in preperation for installing 1/2" engineered Hardwoood flooring and noticed that there is 3/8" "Flakeboard" underlayment on top of 2"x6" t&g floorboards. My question is, is it ok to nail/staple the flooring into the underlayment and 2x6's or do I need to Replace the flakeboard underlayment with Plywood underlayment? Any help would be greatly appreciated.

Definitely not. 1/2 inch engineered hardwood uses a shorter staple and nail length and the penetration is not as deep as a standard nail or staple used for solid hardwood. It's just as if there was a 3/4 inch flake board underneath. No good fastener holding capabilities. Replace or go with a floating method.