Hello,
If you need to make your old cert/key pair "dissapear" (which is odd, I've also never heard of that), you can simply create a self-signed certificate to overwrite the old pair.
User Level -> SSL Certificates -> Create your own self signed certificate
fill in the info, and save. This will overwrite the old cert/key pair.
Also, changing the SSL option to "Shared Server Certificate" will change the SSL options in the VirtualHost to use the Server's main SSL cert/key pair.
Make sure that you didn't also set the domains cert/key pair as the shared server's pair as well..
again, creating a self-signed certificate should fix that.
John