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Hi Fedler,
Thanks for reaching out to us here. I can understand your concerns with incorrect amounts remaining in your QuickBooks Desktop Payroll. You are correct in your thinking, as making changes can have a negative impact on other areas of your books, such as source deductions, reconciliations and others. For this reason, speaking with an accounting professional for their expertise is the best course of action, to ensure a positive outcome on your books. If you don't have an accountant, you can search for a ProAdvisor in your local area by following this link.
If you have any other questions, please don't hesitate to reach out. We would be glad to assist!