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Using the ArcToolbox tools, a Python script, or the Field Calculator to update feature classes participating in a check-out replica does not update the parent ArcSDE geodatabase upon synchronizing the check-out. Using these tools within ArcMap while editing the check-out feature class is the only way the updates will synchronize.
When creating a check-out replica to a file or personal geodatabase, system tables are created in the check-out geodatabase. These system tables keep a record of the edits that have been made, so only the edits are sent to the parent ArcSDE geodatabase upon synchronizing (checking in) the check-out replica.
However, the system tables are only updated if changes are made to the check-out feature classes during an ArcMap edit session (or at versions 9.3 and 9.3.1, using the Simple Data Loader in ArcCatalog). For example, if ArcToolbox tools, a Python script, or the Field Calculator are being used to update the check-out feature class outside of an ArcMap edit session, then the changes are not loaded into ArcSDE upon synchronizing the check-out.
Below are three possible ways to update records in the check-out file or personal geodatabase feature classes and synchronize those changes back to ArcSDE: