Cherry Blossom Spell causes 2 ability score damage to either your physical or mental ability scores whenever a spell attached to it causes damage. Excruciating deals 2d6 nonlethal damage each round with an additional point of Dex and Con damage. It doesn’t specify whether it only procs once or what kind of damage triggers it, so I’m assuming yes, it does work each round and it stacks with the pre-existing ability score damage. It might not be the most practical way to deal Con damage, but it sure sounds sadistic.
They would stack.
That said, Trial of fire and acid is a better spell for cherry blossom as cherry blossom is triggered whenever the enemy takes damage. Excruciating deformation has it's damage negated on saves, whereas ToFaA still deals half damage which still procs the ability damage from cherry blossom.
But the metamagic feat also comes with a caveat:
If the spell does not normally allow a save, the target can attempt a Fortitude save to negate the effect.
So that’d imply that the cherry blossom effect can be avoided if the target makes a save regardless of what spell is used, right?
That's why Trial by Acid and Fire is perfect for the Cherry Blossom metamagic.