How to Handle a Paid Voided Check?

A vendor was paid twice on same invoice...one by void check and another by replaced check:

Check # 1 issued on June 14, 2012 for $900,000 and voided in system on June 19, 2012. However, the user never called the bank regarding Voiding of the check.....so bank cleared Check # 1 on June 22, 2012.

Check # 2 issued on June 19, 2012 for $900,000 as a replacement of the voided check #1 for the same invoice # and was cleared by bank on June 22, 2012.

So, we have two (2) checks for same invoice in the system one is voided and the other paid. Vendor acknowledged the double payment.

However, we have three (3) invoices that amount to $900,000 which have NOT been keyed into system.