There is a few ways of migrating APs from one to another. It all depends on how the APs discover the MM in your environment. You can always adjust the DHCP Options/DNS records and reboot the APs. Failing this, you can also using the AP Provisioning page to re-direct the APs to the other controller.
The commands you've specified will only remove them from the db of the respective controller. The AP will still be provisioned with its configuration and will still attempt to locate this controller thus creating an entry in the db again.
Maybe you could provide some more information on your environment? Is both sets of controllers managed by the same MM or different MM's? How do the APs discover their controllers?