Basically you can change most network settings - including vMotion - without affecting the VM's. When you say they reconfigure the VLAN, do you know how long this will take and whether the current VLAN will be available during this time? In this case you wouldn't have to implement any workarounds, but just update the VLAN on the ESXi hosts' vMotion port groups.
André
PS: About your question "Will the loss of connectivity on only the vmotion port cause any kind of isolation response, failover, etc.?"
No, it's only the Management Network which is used for HA, so all you loose is vMotion/DRS.