The Enterprise and everything inside it would have been re-organized at the molecular level, adding to the available matter used to create the structure of and lifeforms on the Genesis system. A lot of people forget that not only was a planet created but also a star.
Do we know that the star was created by the Genesis torpedo detonation? There was a visible pulsar inside the Mutara Nebula during the Enterprise-Reliant
confrontation. Moreover, there's no sign of the class-D planetoid that was previously adjacent to the nebula.