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SAP BI - What are the Setup Tables?

The Setup Tables are the objects from which the Business Warehouse system is going to extract data for Full loads and Initialization on LO DataSources.

When a Full extraction or a Delta Initialization is going to be performed, the Setup Tables need to be filled with all the historical data to be loaded to the Business Warehouse system. This ensures the extractors won't need to access the always busy application tables (like EKKO or VBAK).

Their content can be deleted any time, without affecting the R/3 transaction data.  In fact, after the full/Init load has been performed, it is highly likely that the information contained in the Setup Tables is already not up-to-date anymore. Therefore, it would be no harm at all to delete their content. You may think of it as a "PSA" on the R/3 side.

If the load performed was an Initialization, the next records to be extracted will be sent to the Delta Queues.