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Yes. The documented behavior matches what is happening.
For each calculation profile, when a new calculation is run, the previous calculation errors and the emissions related to the activities are deleted. That means running one profile can remove previously generated emissions before recalculating its own output.
Also, if calculations are configured to run automatically after data ingestion, each connection refresh can trigger a calculation job as soon as that import finishes. The documented guidance is to separate imports and control the order when calculations run automatically, because calculations can start before all required data is in place.
Based on that, the supported approach is:
- Review each calculation profile in Calculation profiles.
- Edit the profile and check whether Automatically run this calculation when data is refreshed is enabled.
- If the goal is to keep emissions from multiple activity imports available together, disable automatic calculation on the separate imports.
- Complete all required data imports first.
- Then run the calculation profiles manually in sequence from Calculation profiles by selecting the profile and choosing Run calculation.
- After each run, use History on the profile to review the associated calculation jobs, last run time, success rate, and any errors.
For tracing what removed emissions, the supported visibility in the documentation is the calculation profile job history:
- Go to Calculation profiles.
- Select the profile.
- Open History in the right pane.
- Select the most recent calculation job to view error codes and line-item details when available.
The provided documentation does not describe a separate supported audit table that identifies which calculation job deleted or replaced rows in msdyn_emission.
One more relevant point: after existing data is deleted and new data is imported, calculations must be run again so emissions are recalculated for the new activity data.