This solution was provided by Paul Laskow from Advanced Business Advisors.

Although there is more than one way to address this problem in ManEx.  This article describes my recommended solution:

When users discover that the customer used a new customer part number for a specific manufacturer’s part number already tied to another customer part number for that customer, add the customer as a manufacturer.

Then, under the internal number in the inventory item master, quantity tab, add the customer and the other customer part number(s) that all point to the same manufacturer's number.

Do not update all customer's part numbers and BOMs, but selectively go into the selected customer part number and add the customer and other customer part numbers to the AVL under the quantity info tab.

This will add the alternate part number to the AVL for that manufacturer. 

When BOMs are printed, the entire list of customer part numbers will be listed as part of the AVL and be visible for cross referencing on one document.