Harbour air finally combined operations with the new terminal, but they built their own new berth and second gangway.
I believe the fees and a purported safety issue with the height of the berths were the issues.
It's still accessed by the underground road. The space where Harbour Air's separate terminal access was will (eventually) become a restaurant.
Picture of the completed setup:
From:
http://vhfc.ca/about-vhfc/