We received an important reminder today from the product group about manually editing the database, and I wanted to stress the importance of this on their behalf. The SCOM community and our customers need to know that doing so without the direct guidance and support of Microsoft is not supported, and may cause database corruption.
Specifically, they referred to removing computers and other objects by updating IsDeleted=0. This will subtly corrupt the database and cause significant problems in the long term, which may ultimately result in rebuilding the management group with a clean database.
The only supported method to manually remove stuck, stale or otherwise undesired computers and objects is to find the discovery that added it, create an override to disable the discovery for that object and then run the Remove-DisabledMonitoringObject cmdlet using the Operations Manager Shell.