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Why is there a volume quantity difference between the values seen in element properties versus volume calculated in reports?
The volumes are generated by the feature definitions in the civil model. In this example the feature definition is Volumes_Fill. If this feature definition is toggled on, the volumes generated in reports will scan the entire civil model for any features that have this definition, including reference files.
One reason for a difference in quantities could be that an unseen reference has this feature definition in its file and the volumes in that dgn are being accounted for.
You can check this by locating the unseen reference file, opening the dgn, and toggling on/off the assigned feature definition as needed.