Problem: I am using the MartUpgrade utility and my domain user does not appear grayed out and populated in the User Credentials when that is set to Windows Authentication.
Figure 1. r8 source mart connection
Figure 2. r9 Destination mart details
Even though your domain user does not appear, the data is still present for the user who is logged into the Windows OS. Whatever Windows user you are logged in as will be used by the MartUpgrade for the username and password as in Single Sign-On (SSO). Please press test connection and as long as your Windows user is a member of the mart it should work.