hello diogojusten,
FYI,
The set-SR-BR, it uses a scratch register to switch the slot, but it only works after the warm reboot.
The set-active-boot-slot, it uses UEFI variables to switch the slots, it can update BRBCT, so it also can work after the cold boot.
according to above,
nvbootctrl command options, set-active-boot-slot on AGX Xavier it sets UEFI variable via ESP partition to switch boot slot.
please check whether the ESP partition is mounted to /opt/nvidia/esp directory when triggering capsule update by above commands.