Unless agent removed the ATL-TPA segment from the reservation, it will auto cancel remaining flights when don't board. The ticket will also need to have been reissued.

I'm not sure something was misunderstood or agent doesn't understand. However there's no being "marked" for cancellation. It's simple, if you have flight in reservation and don't board, all remaining flights are canceled. Adding a note doesn't fix this. The flight must be removed and ticket reissued.