Can you explain why they still show up even when the appropriate fields are filled out? Is this the way QuickBooks Online is supposed to work? Is there not a way to use classes and locations and pull an accurate Balance Sheet in QuickBooks Online? Maybe I'm misunderstanding but it seems like your saying that if I use classes and locations, I have to pull a report from QuickBooks Online, export it to excel and then manipulate it so that it is correct.

I have figured out that I can create a journal entry where on one line I credit or debit an account and include a class then on a different line I debit or credit the same account but leave off the class it will at least zero out the Not Specified box for that account. Then when I pull a balance sheet, the Not Specified column is "0" rather than blank but that's fine because it's basically the same for what I need and the rest of the accounts are okay.