Models that have replication features added might have to be upgraded 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 suit the current version of Enterprise Architect. After upgrading a Design Master you should re-create the replicas, rather than synchronizing.
If the model is not a Design Master, Enterprise Architect must first remove the replication features, then upgrade the project in the normal manner. The Upgrade Wizard guides you through the steps.