This is perhaps an area in which conservationists may contribute.
It seems that the confusion is due to different usage of the word "endangered" by two entities, the CITES (which protects species from over-exploitation through international trade, and which forms the backbone of Hong Kong Law Cap 586) and the IUCN (which produces and maintains the Red List of Threatened Species, which "is widely recognized as the most comprehensive, objective global approach for evaluating the conservation status of plant and animal species"), and apparantly there is lack of communication between these two entities.
However, I notice from AFCD website that AFCD (or HKSAR Government) can initiate amendments to CITES Appendices I, II and III. Perhaps conservationists of Hong Kong can discuss with AFCD so that the Red List species relevant to Hong Kong can be appropriately incorporated in CITES, and accordingly enacted under Cap 586. However, please note that both CITES and Cap 586 only focus on prevention of over-exploitation through trade (import, export etc). In the longer term, perhaps more should be done to effectively prevent the endangered species from extinction.