Since QuickBooks Desktop will not allow a negative deposit, the resolution for this issue will depend on whether or not a refund check has already been created in QuickBooks Desktop.
To remove a negative entry from the Payments to Deposit screen in QuickBooks Desktop that was created by a return or receipt reversal in QuickBooks Point of Sale for Desktop, follow one of the options below:
If a refund check has already been created and is in the checking account register:
NOTE: These transactions remove the negative entry on the Payments to Deposit screen while keeping the payment in the checking register.
If a refund check has not been issued: