Looks like Harbour Air did get a small concession from Pavco, which originially demanded for rent and a $12-per-ticket fee. Now the an extra $9.50 will be added to fares for each flight. The move will happen at the end of this year. It is not known whether Harbour Air still have to pay the rent. Also according to some news report, Harbour Air will now spend $2 million to build an extension to the centre's docks.
I don't think Harbour Air lost any money during this saga. Instead the new terminal operator lost a lot of money every day due to the underutilized facility.
Source:
CBC News