At this date I would assume you have finished your project, so this is parenthetical.

I assume you are an ME student.

In the real world, you would exactly what has been suggested, but I will refine that a little. You will design the piping system, pumps, fan coil units, etc. You, as the ME, will specify the requirements of the chiller/s for the contractors to bid on. You let them choose what chiller package/s they want to submit and this includes the choice of refrigerant. They will do this based on what they have access to and cost of same. And as Iceman pointed out, you want to reserve the right to re-evaluate on the basis of what they preserve.

Or, to put it another way, trying to pick the specific refrigerant for a large chilled water system in the design stage is putting the cart before the horse. Design the system and specify the chiller requirements. What specific chiller configurations, including refrigerants, will be dictated by what is available in your area.