It only matters if u get prompted to replace files when u ran setup.bat and you typed Y (for yes) instead of N (for No). You will find the nvapi directory in the location you placed the files, something like UnrealEngine-4.9.1-release\Engine\Source\ThirdParty
vapi. You will need to replace them with the contents from the zip in the same location (or revert them if your using a github fork)