In one embodiment, a first multiple spanning tree (MST) region configuration for an MST process may be maintained at a switch in a computer network, where the first configuration has a virtual local area network (VLAN)-to-instance (VI) mapping that maps each of one or more VLANs to one of one or more MST instances in the MST region. The switch may subsequently receive a second MST region configuration that has a different VI mapping than the first configuration, and may determine one or more VLANs of the second configuration that have a different VI mapping from the first configuration (“affected VLANs”). Accordingly, in response to a trigger to apply the second configuration at the switch, the affected VLANs are blocked for a delay, and the second configuration may be applied at the switch without restarting the MST process.