The City's basis in the Shipyards is the $36.5M given to TriLegacy. That's it. It owns the Shipyards strictly as a secured creditor (oh, and under state and federal regs, as a secured creditor, it becomes entirely liable for the contamination if it does not actively try to convey the property in a commercial feasible manner).
Under Khan's proposal, the City's basis in the property is $36.5M plus whatever capital costs Khan is seeking. Seems to me, the 20% that goes to the City plus future tax revenues eventually covers the City's basis in the property.
If the City breaks even on this deal, it's a win. That property has been idle for far too long.