Fixing how the deposit was applied to the invoices is the best solution, as I said in my original response. It is not hard to fix mistakes in QuickBooks. I would also be careful about transaction dates, as QuickBooks will default to the current date for a new transaction. It is important to not let your payments or credits get applied to outstanding invoices in the wrong period. You will not mess up your bank reconciliation if the amount of money received is the same after you fix how the deposit was applied to the outstanding invoices. It is not recommended to post a deposit straight to accounts receivable on one day, and then apply credits on customer accounts on a later date, especially if you cross over months, this will mess up your reconciliation.