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When synchronizing a replica, system versions are created and removed. When an acknowledgement message is received, system versions that are no longer needed are removed. With this bug, however, there are some cases where they are not removed. Leaving these unneeded system versions can have an effect on the compress process.
This is a known issue.
Exporting a data changes message triggers the logic to remove the unneeded versions. Run this any time after receiving an acknowledgement message; for example, when sending changes using connected synchronization or when receiving an acknowledgement message explicitly.
Since the message is being exported for the purposes of deleting the system versions, it is not necessary to send the message. Any changes in this delta file will be sent again with the next synchronization. It is also possible to set options to export the message without any changes. The following describes how:
There is an ArcGIS 9.3 Service Pack 1 patch that addresses this issue.