Models that have replication features added might have to be handled differently from regular projects.
If the model is a Design Master (the root model of all other replicas) then you can upgrade the model to the current version. After upgrading a Design Master you should re-create the replicas, rather than synchronizing.
If the model is not a Design Master, the model cannot be upgraded in the normal manner. First Enterprise Architect must remove the replication features, then upgrade the project in the normal manner. Use the Upgrade Wizard to guide you through the steps.
The Upgrade Wizard should handle the upgrade process for you, and detect which upgrade method is the best.