So that I'm able to provide you with the best resolution, could you please verify with me the specific bank accounts that were not updated?
Here are a couple of suggestions you can try:
Manually update the bank account
Click on the Banking or Transactions tab.
Locate and select the bank account.
Click on the Update button.
Enter your bank sign-in info in QuickBooks
Click on Banking, select Transactions, then select Bank transactions.
Locate and select the bank or credit card account you need to update.
Click on Edit ✎.
Select Edit sign-in info.
If your web browser auto-fills the user ID and password fields, clear them. This ensures your browser doesn’t put in old info by mistake.
Manually type in the user ID and password for your bank account. If your bank offers a Show option, select it so you can confirm you entered the password correctly.