Thanks for taking the time to reach out to us. I'm here to provide some insights and guide you to the right support so you can get the help you need.
Once you made changes on your Merchant Service deposit account, the QuickBooks Desktop deposit payment should automatically be updated since both of them are connected.
In this case, I encourage you to contact our Merchant Service Team so they can take a closer look at this issue. They also have necessary tools to further assists you throughout the process of setting up the correct account for depositing your merchant service payments.