To download the code to the controller, the APs will not be affected. However, a reboot is required to load the new code, and when you reboot the WLC, the APs will disassociate.
When they reassociate, the APs will download the new code from the controller and reboot. This process takes several minutes, so schedule the appropriate amount of wireless network downtime.
Since APs can bounce around from controller to controller, make sure you're running the same version of code on every controller. If they're different, anytime an AP associates to a controller with different code it will need to go through the download process.
In addition to Jeff's comment, upgrade the backup controller first (if applicable). Rule of thumb in our network is to find a controller with the least amount of associated AP's and upgrade that FIRST. Then roll it across one by one.
I do hope you are also upgrading the bootstrap accordingly.
"If I was to upgrade the DC controller, will the ap's in HQ (pointing to DC as secondary controller) try to get the updates"
No, the AP's won't do that. The AP's will only "swing" if the primary WLC's go down. The AP's primarily associated to the DC will "swing" to the HQ WLC until the DC WLC comes up. When this happens, the AP's will swing back, upgrade the IOS and reload.
If you are going to do multiple reboots to a WLC, I recommend that you enable the service port and disable the Management Interface. This will prevent the AP's from corrupting their IOS.
Otherwise, you'll have to upgrade, boot, wait for all of the AP's to join, upgrade their IOS, boot and then load the next firmware to the WLC. This will take alot of time.
Transferring Crash file from standby: Login to the Active WLC in HA.
From CLI: (Cisco Controller) >transfer upload datatype crash (Cisco
Controller) >transfer upload filename (Cisco
Controller) >transfer upload mode tftp (Cisco Controller) >transfer
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