You can move a payment that has been incorrectly applied from one customer to the correct customer, if the payment has already been deposited and reconciled.
You can also use this process to correct any customer payments that were entered through the make deposits screen and are not connected to an invoice.
Performing the following steps in QuickBooks will correct these issues and allow the reconciliation to remain intact.
To correct a misapplied payment:
The payment has now been applied correctly and the reconciliation left intact.
Correcting Deposits made through the register or through the Make Deposits window that were not applied to customer payments:
The payment should now be correctly applied to the deposit.
If this solution does not resolve the issue, review other available QuickBooks support options for additional guidance. You can also read and post messages relating to your issue on the QuickBooks Community forums.