AR payments apply to the incorrect invoices

We have a big problem and hope someone on this forum can help. Our AR manager just left our company a few weeks ago. We just ran our AR Aging last week and found one of the accounts has a big amount past due, so we decided to collect the debts. When calling the customer and ask if they could pay one of the invoices, their respond was, we already paid that invoice, even showing us prove that invoice was paid per check #. It was embarrassing so we decided to do some research and found that our AR manager was apply that check # to a different invoice. We then decided to go back further, and found that she has been apply recent payments to the oldest invoices for years. This account is a big account, and I'm talking about million of dollars per month, where the customer ACH a payment, paying for multiple invoices. So now there is no way for us to reconcile which of the invoices hasn't been paid. Have this ever happened to anyone on here, and how did your company going about reconcile the differences. Please help us. P.S. This is a long time customer going back for years. Also, normally when the customer ACH a payment, they also e-mail us the remittances, stating the payment is for these invoices etc... etc...however, she has been deleting her e-mails, so we have no way of tracking it down. We want like to call the customer, but don't know what we should ask. We know the customer is using Oracle Accounting Software. Thanks!