If it's an HH guitar with a five-way switch, the magnet probably does need to be flipped - if you're using (say) the inside coils of the two humbuckers and you want it to be hum-cancelling.
If it's HSH it probably doesn't need to be flipped because you're only using the split humbuckers in conjunction with the middle pickup.
It's flipped in the sense of turning the magnet 180 degrees (without moving the pickup, of course) - so the end of the magnet which was pointing north (or east) is now pointing south (or west!)