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Thanks for reaching out to us, @Pinnacle VS.
You can exclude the transactions that can be found under Batch actions from your Banking tab in the two separate QuickBooks companies.
Let me share the steps on how to do it below:
I've got a great article for you that provides additional details on excluding transactions. You can view it by clicking this link: How to exclude expenses from downloaded bank transactions?.
For future reference, check out this article on how to review bank and credit card transactions after you download them: Download, match, and categorize your bank transactions in QuickBooks Online.
Drop me a reply if you have any follow-up questions about excluding transactions. I'm always happy to help.