Why did you think of doing something like that anyway , wether it's similar or unlike polarities (the pick and the pickup) the magnetic field will certainly affect the motion of the magnetic pick , making it harder to control.
The magnetic field will also dampen the strings quicker , that means less sustain .

I'm not sure, but I don't think it's going to leave a permanent effect on your pickups magnets ... As I recall, magnets can be demagnetized by extreme heat , hitting them very hard and other stuff I don't remember.