If I have a Ditto (Legends Awakened #27) as my active Pokemon and my opponent's Active Pokemon is a Rampardos (Platinum #13), would Mold Breaker cancel Ditto DNA, or would Ditto still "be" Rampardos?
I think you mean "Iron Skull".
All that Iron Skull does is prevent anything from changing how much damage is done.
It doesn't stop Ditto from having more Hit Points.