Thanks for the info Mark. I'm not seeing the custom data being deleted though by the scheduled daily scans but a full sync does definitely delete it. So possibly I can get a rough esitimate of the settings out there if I send down a package to run inventory scan as user and collect the info.
I've noticed there is also HKU. Have you used this before? Does it skip the SIDs and show the info under the users somehow. From what you say using the HKU would essentially be useless unless the exact SIDs are known.