The British Steelies Society

More likely you magnetized the strings which can happen easily but that's a simple fix change the strings. I know that because if you fool around enough with a ebow or other electronic magnetic toy you magnetize the strings, not ruin the pickup.

Can the EBow damage my pickups?

The EBow produces a very weak magnetic field. Not much more than the field generated by the strings themselves when a chord is struck. The source of this weak field sits above the plane of the strings, a good distance from the magnets in your pickups. It takes a pretty strong field like that produced by an AC powered soldering gun to affect the magnets in your pickup and even then the gun must be close to the pickup.