We received an item in PO-C and were invoiced incorrectly for the item, but the incorrect invoice was processed in AP-C before the overcharge was noticed.
 
We were credited for the overcharge and I know we can enter it as a credit memo in AP-B but the correcting invoice which was a credit for the overcharge has no relationship in Evo to the original receipt and AP-C.  How do we make sure that the last and average cost of the item is correct?

What I usually do is make 2 entries in Accounts Payable.
 
In this situation, first reverse the first invoice entered in AP-C, by entering the invoice number and respond, yes, to the question - do you want to reverse this invoice.
 
Then I enter in AP-C only the properly billed price from the first invoice which shows the incorrrect price.
I.E.  if I was charged $12 each instead of $10 each, I would enter the $10 price in AP-C.  This ensures inventory has the proper cost.
 
Then I make a second entry in AP-B for the $2 overcharge times quantity received.  The total of these 2 entries equals the incorrectly billed invoice.
 
When the credit memo arrives, I enter the credit memo in AP-B for the $2 overcharge.
 
This way ensures the Vendor's Accounts Receivable can match the invoiced amount and credit memo amount on their set of books when I remit payment.  The payment stub will show the total amount of the incorrect invoice (though 2 entries) and the credit memo amount.