Virtual Knowledge Graph (VKG) is known as a data integration paradigm used to efficiently manage the heterogeneity of richly structured data that is common inside several organizations, in inter-organizational settings, and more openly on the Web. Although such a paradigm continues to gain importance in both foundational and applied research, updates in VKG systems remain an open challenge that has received less attention. Yet, a solution to such a problem would be of great importance, as it would allow VKG systems to be full-fledged, thus allowing end-users to fully manage source data through the lens of the ontology they are exposed to. This research aims to propose a comprehensive framework for instance-level updates in VKGs, where updates posed over the ontology have to be translated into source-level updates and, more importantly, how the side effects related to the propagation of ontology-based updates to the underlying data source can be minimized.