Sonic X is a Japanese animated series based on the popular video game series, Sonic the Hedgehog. It is the 4th Sonic TV series as well as the first anime. The show aired from April 6, 2003 to April 18, 2005 with 3 seasons(78 episodes total).
Sonic's planet has a slower time than Earth
This is actually a fact.
On Sonic X season 3, Christopher Thorndike ages normally and becomes and adult. This season is set 6 years after season 2, and when Sonic and his friends and enemies finally returned to their home planet. Chris' friends and family had also become older within those years. One day Chris recalls that he had missed Sonic since he returned home, he builds a portal that brought him to the planet, but it also turned him from an adult to a child again.
Meanwhile in Sonic's world, it has been only 6 months since season 2. This states that time in Sonic's planet is slower than in Earth. In real life, some planets in the Solar System revolve around the sun slower than Earth, which means Sonic's planet behaves like this.
When Chris returned to Sonic's planet he connected with the planet's time, which turned him back into a child.
The seeds are actually souls.
In the season 3 finale, Cosmo transformed into a powerful form which helped her destroy a terrible gravity surrounding the planet egg. She announced to everyone that the only way to restore her clan and the seeds was to have her be killed with the Chaos Emeralds and the Master Emerald's power. Tails was in grief because how much he loved her, but he learned that destroying her would save, him, his friends, and the whole galaxy. He fired the cannon that destroyed Cosmo and the planet egg forever. Tails then sees a vision of Cosmo and shares his love one last time. On the aftermath, Tails looks up to the dark sky and sees Sonic. Sonic gives Tails a seed. He tells him that the seed was all that was left of Cosmo, which makes Tails mourn about her loss.
At the final episode of Sonic X(The Place Where Planets Are Born, or So Long Sonic), Tails had planted the seed and it is seen to have recently sprouted from the soil. It's possible if Cosmo's seed is actually her soul and growing the seed will resurrect her. This may refer to Groot's rebirth in Guardians of the Galaxy.
Eggman probably killed Chris
On the Place Where Planets Are Born(or So Long Sonic), Dr. Eggman built a pod called, "Hurry and Go Home Version 1"(it's name in the Japanese dub), which can take Chris back to his home planet in just 3 minutes. The pod can travel between space and time as it travels from Sonic's dimension to the Earth dimension, once it returns to Earth the pod will be useless forever.
Eggman predicts that he will return to earth after a week since Chris entered Sonic's world or it could be 10,000 years. He was also concerned if his body will change or not, but Chris accepts the ride since he had done everything they could to save Sonic's galaxy. Chris rides the pod and leaves the planet forever. His fate is left unknown due to the end of Sonic X.
If what Eggman said was true, Chris may be dead once the pod returned home, otherwise he might survive. What is actually true is that Eggman built this pod so that he could undermine Sonic's team and would never have to worry about Chris again, whether he lives or not.