First, the master website is any domain or subdomain that does NOT appears as a slave site.
I don't know if you are using the same account (ie cPanel account) for the domains but in this case, you could resolve the relationship between the domain name and the "document root" to point on the existing place. (In cPanel, you can use "Addon Domain")
If you manage the virtual host manually, just define the mydomain2.com to point on the existing document root of mydomain.com.
In JMS, you just have to change in the slave site definition the list of domain and subdirectory for which it is assocated.
The definition of the JMS "Manage site" and "virtual host" must match.
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