In one example, a method includes by a Software Defined Networking (SDN) controller, receiving one or more virtual routes to virtual interfaces from a first virtual router agent managed by the SDN controller, the one or more virtual routes received via a messaging protocol session between the SDN controller and the first virtual router agent; storing, by the SDN controller, the one or more virtual routes to a data structure; in response to determining the messaging protocol session has closed, marking, by the SDN controller, the one or more virtual routes in the data structure as stale without deleting the one or more virtual routes from the data structure and without withdrawing the virtual routes from routing protocol peers of the SDN controller; and subsequent to marking the one or more virtual routes as stale, sending, by the SDN controller, the one or more virtual routes to a second virtual router agent.