QB Issue Resolution:

So just figured this out, you can do this by creating sub accounts.

 

First follow this guide to create sub accounts.   I didn’t create any parent accounts, I just created a few sub-accounts under the pre-generated parent account “Checking”.

 

Then add the bank accounts to those sub accounts you created under Checking, do not select the parent account “Checking” itself during this process.  If you previously connected bank accounts to parents, you’ll have to disconnect them and start over.

Resolution for Issue 'Can I connect multiple checking accounts from the same bank?' available: Yes (Solved).
Source: Intuit Community forum.

Can I connect multiple checking accounts from the same bank?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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