The USB settings for the access points are in flash, so those are persistent.
As a tip, if you want to move RAPs from one controller to the other, you could export and then import the local database into the new master. The RAP whitelist is a table in the local database and cannot be separated so, all your local users, guests, mac addresses, etc will be exported/imported as well.
After that is done, you can use a provisioning profile on the old controller to burn a new master ip address into the flash of the existing access points. A provisioning profile can be added to an ap-group and will overwrite whatever was previously provisioned for that RAP. In your case, you would only want to override the master ip address, so you would attach it to the ap-group of your raps that you want to migrate and it will write the new ip address into flash onto those APs. Setup a test RAP ap-group and apply the provisioning profile to that and see what happens.