Cherrim AR

[Lord Yabol]

I have an active Scizor SF and benched Shaymin lv.X (+40 HP), Cherrim AR.

Opponent attacks with a water Arceus.

This attack wouldn't be affected by Scizor's body, but how about Shaymin's and Cherrim's?

 

[PokePop]

Cherrim is trying to reduce the damage done. It is ignored by the water Arceus' attack.

The attack isn't affected by Shaymin's Body.
On the flip side, Shaymin's Body isn't affected by the attack, either.
One does damage, the other raises HP.
There is no conflict here. How much HP a Pokemon has doesn't have anything to do with how much damage an attack does.