These objects should be reviewed individually to check if they could be duplicated, or just having the same name, so you can modify it prior to the upgrade if needed. In the warning message, it is included the XID of both objects, and the current name.
To illustrate that according to the sample given, running XPSExplorer, you need to modify the real name to be different each other :
CA.SM::Realm@06-0e9046e2-864a-105a-98a3-84d3c46c002a MyRealm
CA.SM::Realm@06-4ab90e77-7714-103c-a18d-84d3c46c002c myrealm