This serves the same purpose as the deleted scenes from Hikaru the Kitsune: A Future Hope.
Don't mind the lame deleted scene title. Anyways, the reason why Silver is not in the story is because he returned to his point in time.
Clara, on the other hand, is just sticking around for a little while before she does the same. Except... well, let's just say a certain something changed that plan.
"You sure you want to stay in Light Mobius?" Silver asked, frowning.
Clara nodded and said, "I'm only going to stay for a limited time."
"Why?" Silver asked quietly, somewhat confused. Their job was done. And to him, it was time to go home.
"Silver, please." said Clara, placing a hand on his shoulder. "I promise I'll come home once my time here is over. But for now..."
She trailed off. Unsure of what else to say, the black-furred echidna hugged the silver-furred hedgehog.
"Hey, you do what you have to do," Silver replied, hugging her back. "If you have to stay, then stay. I won't make you leave."
Clara pulled away from the hug. "Goodbye."
After saying her goodbye, she ran off to Castle Mobius.
Silver pulled out his Time Stone and vanished in a flash of gold light. ________________________________________________________________________________