Publish As Built
Use this tool to save design data in as-built tables in the geodatabase.
Click the Publish As Built 
icon
to commission the design. If any design validation issues exist, you
will be notified that the issues need resolved before the design can
be commissioned.
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You can control whether or not a confirmation prompt appears if your design is about to overwrite nodes in the GIS. See Settings for more information.
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As it states in Settings, if you check both prompt options, you are only notified if the publish action is going to affect adjacent or non-design nodes. If that is not desired, cancel the publish. Then, import those adjacent, non-design nodes, resolve any conflicts, and publish again as a complete set.
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The scenario where nodes are inadvertently removed from the GIS is typically seen when you Publish As Built after removing a power jumpering (via a node upgrade or similar operation). The prompts do not prevent you from removing the adjacent nodes, but they help make it more obvious and give you a chance to cancel the operation.
If you don't want to commit the design but instead place the data
in a proposed state, use the Publish Design 
tool.