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I have steps to help resolve the Job Retention Scheme payment in QuickBooks, @AlfonsoCalabia.
I'll ensure that the HMRC Job Retention Scheme transaction is labeled as a deposit when reconciling the bank.
Ensure that you don't use same account when recording the Deposit. This way, the transactions will not offset. Refer to the screenshots below for your reference:
For more details about bank deposits, visit this link: Record and make bank deposits in QuickBooks Online.
Furthermore, check out these articles below on how to fix reconciliation error and manage Job Retention Scheme in QuickBooks:
Feel free to ask me if you have further questions about bank deposit and reconciliation in QuickBooks. I'm glad to help you. Keep safe.