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When attempting to reconcile a version, the following error is returned: "Unable to reconcile: the target version is currently being reconciled against."
This error occurs when other applications or users edit the current version or the target version during the reconcile. A reconcile requires an exclusive lock on the data, so no other edit sessions can be open. However, if the target version is the DEFAULT, the DEFAULT version can be reconciled against even when other users are editing.
Object locks are used in a geodatabase to acquire exclusive and shared locks on version objects during editing and reconciling. When an edit session begins, the geodatabase acquires a shared lock for the edit session. Since the lock type is shared, the same version can be edited by multiple users or applications. Once a reconcile process takes place, the shared lock is promoted to an exclusive lock with the condition that there are no other shared locks present.
Promoting the shared lock to an exclusive lock ensures no edit session can begin when the reconcile process takes place and that no other edit sessions are currently editing the version. The exclusive lock is maintained throughout the reconcile process until a post-operation version completes or the edits are saved.
Stop all edit sessions on the target version, and reconcile.
There are certain prerequisites to reconcile a version. For more information, refer to the following document, ArcGIS Help: A quick tour of reconciling a version.