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2010 to 2013 migration - host name and cert issues

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I'm in the process of migrating our 2010 (mail.domain.com) server to 2013 (mail1.domain.com). Domain name is not changing. My issue is the 2010 server has a host name that is the same as the HOST, MX and SAN cert (both internal and external: mail.domain.com, autodiscover.domain.com, etc). I need these servers to co-exist for a few weeks while I migrate mailboxes. I wanted to create a new mail server host name/alias for the entire org that can be pointed to both servers (email.domain.com). What's the best route to do this with the least amount of impact on clients? I have the new server setup and both servers are communicating with no issues (it's installed, that's about it, I can manage everything from the 2013 server), but the new 2013 server is still running on a self-signed cert. I need to get the 2013 server transitioned over to being the head-end but can't do that until I have a new SAN cert in place. I've read all the articles on how to manage the migration, but all the those scenarios are going with the assumption that the MX/HOST records and certs don't match the actual host name of the existing servers when they start talking about making sure the virtual directories are all the same on both servers. Also, by creating a new SAN cert (for email.domain.com) with all the needed names, will that invalidate my existing SAN cert that still contains the current namespace (autodiscover.domain.com, legacy.domain.com, etc)? 

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