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There is an option to 'move edits to base' for data that is registered as versioned. If a feature class that is registered as versioned without the option to move edits to base is added to a dataset that is registered as versioned with the option to move edits to base, the dataset can still be unregistered, but mixed version types are created.
However, if a feature class that is not registered as versioned is then added to the dataset, attempting to unregister or re-register the dataset as versioned fails.
Enterprise geodatabases do not support feature datasets containing mixed version types. The reason the dataset fails to be unregistered or re-registered is due to versioning incompatibility. There are two known defects related to this behavior, logged as the following bugs: BUG-000082521 and BUG-000092111. When working with versioned data, ensure the aforementioned bugs are taken into account.
Register the entire dataset as versioned with the option to move edits to base in ArcCatalog or ArcMap. Follow the steps provided below.
Note: Step 1 is important to prevent edits from being lost because the feature classes will be unregistered as versioned in Step 3.