One of the issues that we saw in OpsMgr RTM is that if you disabled a discovery using an override let say a particular SQL DB, the instance created by this discovery would not be removed. In SP1 we have added a new cmdlet to force the removal of instances for which discovery is disabled using an override. The cmdlet name is Remove-DisabledMonitoringObject. All you need to do to remove the instances is open up the OpsMgr command shell and run this cmdlet. The cmdlet does not have any parameters. Keep in mind that this cmdlet is only available in SP1 RC.