A migration manager (MM) identifies a source group of compute instances (at a first partition of a provider network) to be migrated to an isolated virtual network (IVN) implemented in a second partition. The MM triggers the establishment within the IVN of an equivalence group of instances corresponding to the source group instances. Connectivity between the equivalence group and a first load balancer which was being used for the source group in the first partition is maintained by modifying one or more configuration settings. After a replacement load balancer is established within the IVN, the first load balancer is decommissioned.