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How to Unapply a Credit on a Bill or Invoice in QuickBooks
Published 10/26/2010 | 
If the credit is correct, you can unapply it. Go to the Vendor Center, select the vendor, double-click on the Bill Pmt-Check that contains the credit, and uncheck the box next to the bill that shouldn’t have been paid.
You can do the same thing for invoices by going to the Customer Center, selecting the customer, double-clicking on the Invoice, selecting the Apply Credits button and unchecking the credit.
Written by +Ruth Perryman, CMA, CFE, CFM, MBA
Ruth has provided QuickBooks help to thousands of businesses around the world since 1996. She is an Intuit Solutions Provider, an Advanced Certified QuickBooks ProAdvisor, and a member of the Intuit Trainer/Writer Network. She is also certified in QuickBooks Point of Sale and QuickBooks Enterprise Solutions.
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I had some credits that were misapplied on a payment, so I voided the check. But the credits remain applied to the first invoice I paid and I can’t unapply them through the pay bills screen (there are now no credits showing to unapply). Other than deleting the invoice and the credits and reentering them, is there another fix for this?
Are you sure you voided the bill payment? You have to select Save after voiding it. Go to the vendor center and look for the bill payment to see if it’s $0. If it isn’t, it wasn’t actually voided.
For future reference, you can change which bill a bill payment was applied to on the bill payment itself. If you don’t see bills at the bottom of the check, you didn’t pay your bills properly through Vendors > Pay Bills.