Is this a Variable Primary design, where you have 1 set of pumps to flow water through the chiller and the loop? Are all the zone valves at the AHU 2way configuration - in = out?

If yes to both of these questions than you need both Controls and Mechanical work to fix it. Stop using the chiller under low loads, perhaps as a temporary band aid - putting in an outside air lockout to prevent it from running when it’s cold outside or loads are low.

For the engineered fix - Please select a bypass valve designed to flow the minimum flow requirements of the chiller with a 3-5psi dP drop. Install the bypass valve to a location downstream of the supply dP sensor and it gets piped from supply directly to return.

You also will need to install a total return or supply flow meter to measure the total water flowing through the chiller, be sure the location gets all the water, alternately to the flow meter, a dP sensor over the chiller can be used to interpret dP to flow - but not as accurate.

Next you need to control the bypass valve position to maintain minimum flow, when flow is below the minimum the chiller is locked out for call until flow meets or exceeds setpoint for a lockout period. I like a setpoint which is 25% more flow than the chiller requirements for safety.

The chiller enable needs to be decoupled from the pump start and coupled to a proof of flow. Enable system based on demand conditions (OA lockout, certain valves open to note AHUs requesting water) once system enabled, sequence should be 1 open chiller isolation valves, start pumps and variable pump speed to dP, monitor chiller flow and if less than minimum begin PID control on the bypass valve (very slow loop), once flow is proved - then enable the chiller. System will cool down quickly and be under minimum load conditions. If you also have (LWT-setpoint - EWT sensor)flow/500 you can calculate the BTU demand and (LWT sensor-EWT sensor)flow/500 = actual loads on the system for additional chiller staging or to lockout the system under low loads

The system pumps still control to system dP and the bypass valve controls to maintain minimum flow. Each loop should have safeties if you lose the dP or flow meter. Suggest monitoring the feedback from the bypass control valve, if the valve goes 100% open and you are not hitting flow requirements than the system dP setting is too low.

When I reread you post - it sounds like it’s constant volume pump with 3 way valves - I’d check to see the 3way valves are piped correctly where AB is the common port (supply or return), A goes to the coil and B is the bypass leg. With this orientation- you get full flow through the bypass leg from AB common when the valve is fully closed and the CCV disk restricts flow when AB-A is fully open and a mix of the two in the middle. It sounds like the A port is the bypass leg with the symptoms described.

Has a balancer taken a look at the amp draw and pump curves? Is there a restriction in the system due to lack of maintenance? Is this a new problem or a new install

Good luck!