When mapping multiple types of down payment invoices that go to two different revenue accounts in QuickBooks Online, you will need to make sure they are unique. This is so that the integration does not give you an error on one type of Down Payment and not the other.
When this warning occurs it is because the batch is coming across without a GL Type ID and because the system doesn't see a GL Type Id (Product ID field) it is using the default "Down Payment" value found in QuickBooks Online.
To fix this warning message and still allow multiple types of Down Payment Invoices in Manage you will need to fill out the Product ID field on your Down Payment GL Account. If you populate the Product ID it will populate the "GL Type ID", which will allow for a unique QuickBooks Online Account mapping.
When you are done you will see that you have two different down payment GL Accounts created.