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I would confirm that you do not have a timeframe specified in the Email Performance Report setup and that you have no other smart list filters applied to your EPR. If the timeframe is set to "All Time" and there are no filters, I'm not exactly sure why the 2 reports are showing different numbers. Also, this is assuming you're using Analytics > Email Performance Report as opposed to RCE > Email Analysis.
On that note, how much do he numbers differ? If what I assumed isn't the issue, I would recommend submitting a ticket to support and ask them to dig in.
I've tested it with several different timeframes actually, from a single week to "All Time" and there are always lower numbers with the Smart List than without. Based on the number of sends we do, the difference in total Sent has been as much as 1 million. I'll submit a support ticket and update this thread with their response. Thanks for helping me out!
Do you actively delete records from your database? Email Performance Reports will retain reporting numbers of records deleted after an email was sent. Smart Lists will not. Generally, email performance reports are the source of truth for email reporting. There are many factors that can cause Smart List numbers to differ from a report.
Thanks Steven, that's definitely the reason my two Email Performance Reports were showing different numbers. We've removed a number of contacts after Cyber Monday.