We monitor all services that are set to Automatic startup. We have an exclusion list that ignores Services containing specific names.
So the problem is when we uninstall software that removes a service, we get an alert (the service is not running, obviously - it's gone!).
What is the thing that we need to do on the machine that updates the list of installed services? I think it's Update Lists by Scan.
That is correct, Update Lists by Scan is what you would want to run. (Monitor > Update Lists by Scan)
As a warning, this procedure is very task intensive on the Kaseya Server and not recommended to run on more than a handful of machines at once or on a recurring basis.