I am in the exact same boat as you are. I created a second certificate by logging off and logging on while debugging issues with provisioning profiles. This created a new developer certificate. I read we need to revoke it, since I didn't find any option to revoke and the next best thing I read was to delete the duplicate certificate. I assumed had the backup in my Time Machine and deleted the certificate without an export. Murphy won, I don't have a backup and no certificate now. There is a ghost certificate now on Xcode with "Not in keychain" message. Some of the bundle id I created are now associated with it and wouldn't let me reuse them. Any thoughts on how to get rid off it? I have sent a request to apple through https://developer.apple.com/support/ for revoking but no response yet for my ticket.

and I don't see the inactive one when I run the command "security find-identity -v " in terminal either.