A surge protector *might* help but I wouldn't bet on it.
I bet you fix this with bonding.
Is the ground electrode system in good shape?
That is always the first stop on a lightning call.
Do you know what failed on the board and what the fault path was?
I am betting it is a ground shift between the well and the ground electrode system. If it is not a metal well casing (that should be part of your Ground Electrode System) you could try driving a rod next to the well and bond that to the GES and the control board (hit that first).
Snap ferrite beads on all circuit conductors.
