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Ok, building on my last post on this topic, export/import from/to SDE. I export my SDE using export "XML Workspace Document..." and I'm using the Z File format because of the large size of the database (exported Z files still approaching 10gb in size). Export process runs successful now, and the import process into a new SDE runs successfully but, when I start checking through all the feature classes, some are missing their data. Schema comes across fine though. Can seem to find any pattern with the feature classes missing data.

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