Will neodymium magnets harm my power drill battery?
For one, the magnetic field generated by the magnets are going to be small potatoes compared to the magnetic fields generated by the motor while in use. 
Two, battery chemistry is essentially unaffected by ferromagnetic fields of the magnitudes you'll encounter in everyday life. Thirdly, there exist specialty tools that have a big magnet on them out of the factory, designed for drilling holes in large pieces of sheet metal, and those of course have no problems.

Unless the magnet is strong enough to lift several 747s off the ground, it's not going to have any impact on your battery.