This is an accepted solution.
Nick here from Shopify.
Do you mean there are two emails your store is sending the Abandoned Cart emails from or two emails you are receiving the notifications for them at?
Would you also be able to tell me if the two emails you have in your admin at Settings > General are the same, please? It should be the email that is set at Customer email which sends the Abandoned Cart. You can see where I mean from the screenshot of my test store below:
Looking forward to hearing from you.
All the best, Nick