Confused about where to apply z visa, Hong Kong or New York

Foreign Experts Affairs has granted my son a Working Permit Indicating that he can apply z type in Hong Kong. However Invitation Letter of Duly Authorized Unit indicated that he must apply z type at the Consulate General of P.R China in New York. Will he encounter a problem at the
Chinese Consulate in New York as The Working Permit from Foreign Experts Affairs indicated Hong Kong.
Thank you
Shirley Lau, New York