Earlier I referred to a 208Y120 dry step down transformer with the three wire delta as it's high side.
Today I had time to go have a look briefly at the transformer. The nameplate show it as a 3 wire delta on the 480 side, and the typical 208Y120 on the secondary.
So there's still a wild card somewhere in the 480 system.
Well if loading the phase conductors to the grounding system requires a bit of loading to force an imbalance then I would say it would have to be a WYE load of some kind, about the only way I would know to find such a load would be turning off loads until you loose the Wye balance which is how we found the drier with three 277 volt heater elements tied into a WYE and center point bonded to the grounding system, the bad thing was that if there was ever a first fault to ground by a phase conductor two of the elements would have seen the full 480 volts which would have either taken out its OCPDs or the elements, we unbonded the WYE point and everything was fine, the manufacture was also notified of their instructional mistake.
I still don't see where this should have caused a problem with the circuit board, most electronics are damaged by over voltage or heat or both, proper design of such an expensive board should include over temp shut down and onboard SPD's to prevent voltage spikes from damaging components, had a lightning strike been ruled out? even a near field event can product current into I/O wiring that is not properly shielded, knowing what failed on the board is the first clue to what might have caused the damage, I have done some work at finding damage causes in electronics and there are some tell tale things that can point to a cause if the person who is doing the research knows what to look for.
like if we find I/O circuit damage then I look for shielding bonded at both ends for parallel current problems where input or output devices might be across areas fed from two or more SDS transformers, if this pans out that its not the case then I suspect a near field lightning strike or LEMP that can induce circulatory current into these conductors, if we see power supply component damage then I look closely at the supply source and possible of inductive loads that may produce transients into the power supply system?
May I ask the purpose of this board if it doesn't reveal any trade secrets? you said this is for a chiller which leads me to believe it might be control system to regulate control over temp and flow of the material which could be water or hydraulic fluid or some other medium, this would lead me to believe you have some 4-20ma I/O's as well as maybe some TC's that could be susceptible to induced voltages if the conductors are long, also does it have some VFD motor control and is there proper filtering in the input and output of these VFD's? as VFD's can cause voltage spikes many times the supply voltage.
And as I said before most VFD's do not like being on an ungrounded system.
The above is just a small example of what it may take to find the cause of the board failure, I have dealt in the past with many pieces of equipment that the engineer of it just didn't have an open enough mind to cover all aspects that may cause premature failures as every installation can be different each having its own unique set of design problems that the engineer never took into account at the time of the system design.
A fix could be as simple as having a transformer installed just for this chiller so its secondary can be grounded, not a cheap option but one never the less.
just trying to give you some ideas to work with.