I had this happen, back in 2012. I can't remember exactly how I got rid of the duplicate Sim. After I did though I did clean up my in-game library, as that's where the game can sometimes take Sims from.
It's been said you shouldn't use testingcheatsenabled on and delete Sims, or use Delete Object on them as it could cause save file corruption. It only deletes their bodies, not that data inside the game.
The best way, according to Nraas is to use MasterController Total Annihilation. And remove the Sim(s) from the library.
Click on Mapview > City Hall > Nraas > MasterController > Town > Total Annihilation > X -- From the list of Townies, find the Sim you're wanting to to remove.
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Reference Link:
Duplicate Sims:
https://www.nraas.net/community/Duplicate-Sims