For the first two APs, you may try by rebooting them, upon reboot there is good chance they will associate themselves with the Site-2 local controller first.
In an Active-Active HA environment, controllers will divide the AP load 50:50 and administrators do not have a controller over which AP goes to which controller. In a single physical site environment, this won’t be a problem but in your case it may happen that some APs will adopt to the remote controller instead of the local one, unless you assign the controllers per site.
APs maintain links with both controllers in the HA pair, one link is active whereas the other gets activated to handle the failover only when the first link goes down.
May be you can try by assigning the controllers per site, save the config, reboot the APs and wait for them to come back online and form the links with the assigned controllers. You need to do it on the PRIMARY controller and the SECONDARY will follow the config. Give APs some time to adopt, finish the channel scan and choose a channel after which the radios will appear online.
You should do it during a maintenance window because this activity will required some time.