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What version of Data Modeler do you use? We recommend 18.104.22.1683.
You can have problems if subview is updated/merged before new tables or FKs are processed. It's good to close design and open it again after the whole update/merge process is finished (including resolving of conflicts). Also you should be careful when manually resolve conflicts - some nodes are marked to be deleted so you should uncheck them if you want them to retain in subview.