All aspects of SSL, including the server's certificate chain, are configured on a per-http-listener basis. Therefore, if you want the 2 domains
https://www.mysite1.com and
https://www.mysite2.com to be authenticated with different certificate chains, the corresponding virtual servers need to be associated with different http-listeners.
In other words, the virtual server represening
https://www.mysite1.com will need to be associated with one http-listener, and the virtual server representing
https://www.mysite2.com will need to be associated with a different http-listener, where each http-listener is configured with its own, unique SSL certificate chain.
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