Since the trip unit has been replaced, it is kind of hard to blame the breaker.
Maybe it is a low tech problem. Has anyone checked the neutral & grounding system & all bondng since the lightning storm? Most power quality surveys start with the grounding system.
If the problem isn't related to grounding/bonding, I'd look for electrical noise when the motor is starting. If it is a really large motor, maybe it has a solid state starter or drive that may have been affected by lightning.
I think the only way to get to the bottom of this will be with a power line analyser or recording meters that could narrow down the search.
Few things are harder to put up with than the annoyance of a good example.