That's a lot to chew on. Please excuse my thinking out loud....
Some more discussion on dividing the problem into motor or supply (and by supply I mean in-plant plus utility):
Normally the observation that the location of high current stayed with supply phase vs motor phase during lead swap would lead you to suspect the supply, not the motor.
Normally the observation that the voltage was balanced without the chiller running would lead you to suspect the motor, not the supply.
You mentioned current imbalances on other motors also, tends to point toward the supply since it's not likely all motors have a similar problem.
Put the above together and you start to suspect that it is a supply-based problem which only shows up when you put a motor load on it. perhaps a high impedance on one phase of the supply circuit which doesn't show up until you put a load on it.
But there's another piece - the currents you reported
"1- 2 , 2- 66, 3-510". Obvsiously a HUGE imbalance. (When did it changve from 1- 200 2 - 215 3 - 252 as originally reported?). In fact there is not enough current within phases 1 and 2 to provide return path for current from phase 3. So you have to suspect an alternate return path through a ground.
But if the ground were within the motor, then your swapping lead trick would have left the high current at the same motor lead. UNLESS - the location of the ground was upstream of where you swapped the leads but downstream of where the motor is normally switched on/off. Assuming you swapped leads at motor terminal box, this could be anywhere between the load side of your starter and your terminal box.
Getting a little far into the speculation stage. If there is a ground it shouldn't be hard to find. Start by meggering from motor with all leads attached. If ground detected, then disconnect leads and see which side it's on.
Let us know if you get more info.