This seems indeed strange. I don't know of any physical effect that would influence Flash cells directly via magnetic fields.
I am more of a software guy, but had to deal with Flash relatively often. Mostly in regards to erase/write duration, energy consumption, and erase/write times. Albeit I have no special insight in any vendor's implementation, I think their Flash cells are fairly similiar, only differing in dimension and some process-related parameter.
But having read into the theory a bit, I remember that erase/write required voltages of 9V or more to tunnel electrons onto the isolated gates. While these voltages had been applied externally 30 or 40 years ago, they are now generated on-chip, via charge pumps.
A direct "hit" by e.g. alpha particles is one way to discharge such an isolated gate. But I suspect an inadvertent activation of this internal charge pumps by EM induction would be another. If the susceptibility is caused by the silicon, bonding wire or external wiring is beyond me.
I am not a hardware developer, but know that motor driving circuitry is quite troublesome. EMI can "intrude" via GPIO or the power supply circuitry, causing severe ground level offsets.