If you Access Points are on on dynamic IPa ssignments (DHCP), you can literally unplug and put them in a different VLAN.
The thing you have to keep in mind is each group of access points in the same subnet will form a new cluster and will have its own virtual controller (VC) managing that cluster.
If I was doing that, I would first bring individual clusters up, update virtual-controller-key for each cluster and then add them to Airwave. Depending on your design, you can create a separate folder for each cluster and use templates with variables to maange the configs.