You should be able to unlink your Apple ID from one eBay account -- though first make sure you know your username and password, or else you may have problems trying to sign in to that account again.
Go to your Account Security page to see the options regarding social media linking:
https://accounts.ebay.com/acctsec/security-center
I am not certain if linking an Apple ID to an existing account might have issues if the email address associated with the Apple ID is already linked to another eBay account, though.
