Hey newcomer! Thanks for reaching out to the Community with your question about merging bank accounts in QuickBooks Online.
If you have potential duplicate transactions, I suggest excluding them from the account. This guide will provide you with the steps on how to do so.
If the duplicate transactions keep coming in, then I recommend contacting our Customer Support Team to ensure this isn't an on-going investigation with the system.
I hope this helps. Feel free to reach back out if you need me again. Take care!