Personally I'd say "treat it as if the spell weren't there."
So if the guy with the feat is making a touch attack, yay for him! If he isn't, then that deflection bonus is just going to be treated as natural armor again (which may or may not matter depending on what other items, feats, etc he has).
So if the guy with the feat is making a touch attack, yay for him! If he isn't, then that deflection bonus is just going to be treated as natural armor again (which may or may not matter depending on what other items, feats, etc he has).