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This is working as intended. Registered service items in an organization exists only as a pointer to data located elsewhere. When this item is migrated or restored, it still maintains it’s status as a registered service item on the destination pointing to the same data source. During the Restore/Clone operation (if the data source the service is pointing to has been moved) there will be an opportunity to re-wire the registered service.
At this time, Backup My Org does has an experimental backup option: “Backup Registered Services as Hosted.” However please note that there are many variables to determine the eligibility for certain registered services to be hosted, including (but not limited to) being shared publicly, the item being owned by the organizationsync capability settings, etc.