KRB...If your primary chilled water hydraulic system is some what complex, like 4 chillers, there will be a difference in water flow through Chiller No 1 if all chillers are working compared if only Chiller No.1 is working, pressure drops in common pipes go up because flow goes up when more chillers and associated pumps are switched on. This will even happen when there are 2 chillers only
Make sure the system is balanced with all chillers working. This will ensure more than design water flow throgh the chillers when only 1 is working....ok energy wasteage, unless you have plenty money to spend, in which case the best way to design a system is to have flow metres on each chiller and a VFD on the primary pumps to give the exact water fow through the chiller no matter what the situation is, regarding staging of chillers. You can also get automatic balancing valves which will ensure correct water fow throug the chiller with out the VFD.
Keep a closer eye on your contractor too, be there when he is balancing the system and unseure no body messes with the valve settings after the exercise.
Balancing using pump curves and throtting the pump is OK, thats how Id do it, but check DP across the chiller vessel to confirm the flow rates. Get Chiller vessel flow curves from manufacturer