In P6 Reporting Database 2.0 the ETL process looked to the refrdel table in the P6 PMDB to determine which projects were deleted. The refrdel table could not be cleared out between ETL runs or those deletes would be lost. After the ETL process is run the refrdel can be cleared out. It is important to keep any purging of the refrdel in a consistent cycle so the ETL process can pick up these deletes and process them accordingly. 

In P6 Reporting Database 2.2 and higher the Extended Schema is used as the data source. In the Extended Schema, deleted data is filtered out by the views. The Extended Schema services will handle any interaction with the refrdel table, this concern with timing refrdel cleanup and ETL runs is not applicable as of this release. In the Extended Schema tables (ex. TaskX) there can still be deleted data present. The Extended Schema views join on the primary PMDB tables (ex. Task) and filter out any deleted data.  Any data that was deleted that remains in the Extended Schema tables can be cleaned out at a designated time by running the clean up procedure as documented in the P6 Extended Schema white paper. This can be run occasionally but is not necessary to run often unless large amounts of data has been deleted.