Sorry that this one is more difficult than it should be, it seems we don’t have a way to specify an instance using our command line tools. What I would recommend in this case is following our moving your Octopus Server and Database documentation, then when you need to update your SQL connection string to do a manual update of the config files.
To do that you will need to stop the appropriate Octopus server service, update the database connection string Octopus.Storage.ExternalDatabaseConnectionString in your OctopusServer.config (or OctopusServer-INSTANCE.config) file. I’ve included an extract from an example file below: