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Topology maps are stored per-VHM. This will allow a managed service provider to create VHM's on their company owned appliance, and provide VHM access to customers which does not display data from other customers.
What you're seeing is expected. If a topology map is created under a particular VHM, you will only be able to access it via that VHM, or when viewing "All VHM's" from a super user / primary admin account.