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I understand that you need to correct the Balance Sheet by Class report. I'm here to help you.
The Balance Sheet by Class report shows the balance of each respective class. The reason why it's showing as a positive balance on Class A and negative on Class B is that when you create the journal entry with the clearing account, you also assigned a class to it. You'll want to edit the journal entry and remove the class from the debit clearing account.
This is how it looks like:
I've added an article you can check: What transactions are not supported by Balance Sheet by Class in QuickBooks Desktop?. This will show you what are the transactions that can cause unclassified or unbalanced on Balance Sheet by Class report.
The Clearing Account is used to move money from one account to another account. Here are some of the articles that can help you to properly the said account:
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Keep on posting here if you need more assistance. Take care!