Your best option is to define a JNDI definition of your database in
and reference the JNDI name rather than set the explicit DB connection information in your metadata model. Using data source names, rather than explicit connection information is the appropriate way to resolve this problem. It also makes it much simpler to deploy to different environments (such as test & production) if all your development, test, and production environments have their connection information defined indirectly and all Pentaho tools simply use the JNDI name. It may take some trouble to set this up initially, but you'll be very glad you did in the long run. And, by separating the definition of the datasource from the files exported by the various tools, you'll simplify your life considerably.
You can probably also define a Connection in the Pentaho User Console -> Manage Data Sources, then import your XMI file and associate it with the Connection name and re-export the file--but I have not tried that.
Hope that helps,