Hi James,
We've had exactly the same issue, I believe Netapp moved the metadata from the aggregate into the volume a while back (maybe to ease migrating deduped volumes between aggrs???).
We also have a VMware NFS volume that currently has 1TB of data unaccounted for, the Filer shows 1TB more space available than VMware can see. When I VSM'd this volume to a new volume it shows the correct space usage both on VMware and Netapp. The VSM appears to ignore replication of the metadata but as you mentioned it does get included in snapshots. The difference with this volume is the "sis start -s" doesn't remove the metadata, it was suggested to reset the SIS data but I am reluctant to do this and will just create a new volume and datastore and storage vmotion into that.
We're currently running 8.1.2P1 and waiting until 8.1.3P1 to resolve this and several other issues.
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