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Flags and barriers are present on a geometric network while in an ArcMap edit session. After clicking on Stop Editing, this prompt comes up: 'Do you want to save your edits?' Clicking 'No' results in the edits to be undone and the flags and barriers to disappear.
The positions of flags and barriers are not kept in memory when the edit session starts. When you stop editing and do not save edits, the features move back to their original position, but the flags and barriers don't remember where their original positions were. Therefore, the flags and barriers are cleared when the edit session ends without a save.
Limit your network tracing to outside of edit sessions. Perform traces within edit sessions only to verify connectivity and flow direction.