Board Thread:Speculation House/@comment-27186569-20170521134631/@comment-26397825-20170602051619

Magnets do have an effect on electronics, but often as soon as the magnet is moved away the electronics are fine again. The only exception to this is an extremely strong magnet, which can wipe a hard drive if slowly moved over the hard drive directly, and it doesn't have to make its way through multiple layers of metal that would reduce the effectiveness of the magnet against the hard drive.

So while Pyrrha did throw out a really strong magnetic wave, there's nothing suggesting it was electromagnetic and Penny should have enough layers between her 'skin' and her hard drive/memory core to protect it from being formatted.