Is this a requirement to cross check your tables in SE11/SE16? Have you clicked on "Number of Entries" in Se16?
You should check how your reports are showing correct data or not?
In Aggregate Maintenance screen, select your aggregate and click on spectacles button(Aggregate Data)
How are you saying you got 40 million records in Aggregate? Where did you see this fig? Because it doesn't show the number of records in aggregate. Is it just a guess or your cube data?