Typically, customers want all the customizations that have been implemented in their Microsoft Dynamics NAV 2009 databases to be migrated to their new Microsoft Dynamics NAV 2013 R2 databases. As the upgrader, you must decide between two courses of action: to implement new customizations in Microsoft Dynamics NAV 2013 R2, or to upgrade the application code by using a compare-and-merge process. This compare-and-merge process is known as a code upgrade. You perform the code upgrade before you perform the data upgrade.
The code upgrade is a sequence of development actions intended to fully transfer the functionality of the customer's solution to the new version of Microsoft Dynamics NAV. A code upgrade can also include add-on functionality developed by third parties or objects changed by the customer.