Unfortunately CMK still does not offer an elgeant and simple solution for this case.
For a one-time task, the CLI method is certainly a good workaround. But it has the disadvantage that you can not limit the refresh only to certain services and if you have many sites, it quickly becomes very cumbersome.
In the graphical user interface, you could use the Periodic Service Discovery rule. However, the tabula rasa in the rule always removes all services and the service filter only works for the services that are subsequently added back and last but not least you can only have one Periodic Service Discovery rule per host at the time.
Furthermore you could probably do this via the CMK 2.0 API but this would require some programming effort.