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I have exactly the same issue. If I import the same data into a file geodatabase there are no issues. Do I really need to unregister my data as versioned? That will create other issues for me because we replicate our data to another SDE geodatabase for our users.
Any suggestions would be great.
Here's a document that talks about this scenario:
- Reconcile/post and compress your edits
- Unregister feature dataset as versioned
- Create your topology
- Register feature dataset as versioned.
Be aware that unregistering features as versioned has the potential for data loss if edits still exist in the delta tables.