I've opened up a TAC case to see if they could identify anything and so far they've come back to state that having "ha-on-bkup-lms" enabled on the HA profile configuration, could be the reason for the APs not swinging back to their primary LMS. Based on the description of the command, it seems plausible. I'm going to try testing this out in my prod environment and report back.
HA on Backup-LMS
Starting from AOS-W 6.4.4.15, a new parameter, ha-on-bkup-lms, is added in the HA profile to enable or disable the HA on Backup-LMS. When this parameter is enabled, an AP can set up a standby tunnel after the AP rebootstraps to Backup-LMS. However, in this case, LMS preemption will be ignored. When this parameter is disabled, the AP cannot set up a standby tunnel after the AP rebootstraps to Backup-LMS; the AP will rebootstrap to LMS if LMS is back and LMS preemption is enabled.