User blog comment:Miskos3/Fairy Tail 531: Pegasus vs. Black Dragon/@comment-6401212-20170415012307/@comment-7418318-20170415081213

Whether the Seed's destruction was metaphorical or literal, either way it wouldn't revert changes that had already happened to his body.

Imagine it this way: The Dragon Seed is a syringe containing a serum that will change the body. Half the serum has already been injected into his body and turned him into a Dragon Slayer.

Now Natsu went and crushed the syringe spilling the remaining serum onto the floor, preventing any more of it from getting into his body and causing further change... but the half that is already in his body won't suddenly be drawn out of his body just because the syringe is broken now.