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When I run the rebuildreportingdb.aspx tool, it deletes all existing marketing definitions (Segments, GoalDefinitions, etc. tables) from secondary reporting database. I came to know about this after checking logs as below:

[Experience Analytics]: SegmentProcessor cannot execute. No segments were found

Before running this, I am deploying all marketing definitions, and they exist on both Primary and Secondary databases. MongoDB is also connected to the instance.

What am I missing here?

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that is exactly what should happen. It's part of the notes on the official rebuild reporting database instructions (https://doc.sitecore.net/sitecore_experience_platform/setting_up_and_maintaining/xdb/server_considerations/walkthrough_rebuilding_the_reporting_database):

When you run the rebuild process (synchronization), this erases all information in the Sitecore_Reporting_Secondary database. Therefore, you should always use a clean copy of the database when you rebuild the reporting database because this speeds up the rebuild process and uses fewer resources.

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