Permanent skills will always reduce the amount prescribed even in battle.
Say you have 80, without a permanent skill, you would have 40 in battle. But now let's say you're using mermen gear. No battle would be 62, you would think that in battle you'd get 31 but in that case the mermen skill only consumed 9 points (40-31).
But what actually happens is that you would drop from 80 to 40 (in battle) then the mermen substract the mana regen, which makes you have 22 points, making it seem like battle is reducing more than 50%.
Gladiator's post in Question regarding Mana Regen System was marked as the answer