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Do you have to model one integrated WSE for the chiller loop, or can you model one non-integrated WSE for each chiller? If the second option is ok, place one HX just before each chiller. Both HXs will receive the same condenser water from the condenser loop, so On/Off sequences should be the same.

If not, I'm afraid you may be stuck using EMS to override the availability of the second chiller. Trying to alter the Plant Equipment Operation Scheme will affect the operation of the entire plant, including the chiller pump and WSE. This won't work for your application since you want the WSE to operate while the chillers are off.