You don't need to flip the magnet to be noise-cancelling with this setup... put it back the way you found it and you should be fine for noise cancelling. RW/RP doesn't really make much sense to me for humbuckers because they possess two coils, and one COIL is already RW/RP compared to the other.
Here's the kicker... are they both S-D pickups? If so, then they are designed to work in opposites... one having the North on "top" and the South on "bottom," and the other having the North on "bottom" and the South on "top." Splitting them in opposite ways (one North and the other South) WILL yield noise-cancelling, but they won't be inner coils or outer coils... just two "tops" and two "bottoms."
If you want to make them inner and outer, just flip one of the pickups over (so the logo is upside-down in comparison to the other one) and you'll have it.
If they're not S-D's or are from two different manufacturers, I would need to know specifically which pickups they are in order to look up their orientation and help out.
Hope that helps.