User blog comment:Miskos3/Fairy Tail 535: The Greatest Power, Review/@comment-24039234-20170513181647/@comment-7418318-20170513205058

The way I understood the seeds is that now that they are destroyed (if they really are destroyed, rather than their seeming destruction being something metaphorical) they can no longer inflict further change on Natsu, but the change they caused in the past already happened so it'll stay on Natsu regardless of whether the seed is present or not.

Imagine it like a syringe. If you inject someone with half the serum and then break the syringe, it'll prevent the 2nd half from doing anything, but the first half is already in the person and won't flow out just because you broke the syringe. That's how I see the seeds.