It's nice to see you here, derekc123!
Yes, you'll have to continue paying for the employer portion of the Social Security and continue deducting the employee portion from his pay.
The wage base limit is independent per employer. If your employee has reached the limit and paid the SS in excess because he has two employers, he can request for a refund. He can reach out to a tax advisor to recover the excess.
Feel free to reach out if you have other questions.
