The firmware update will default the boot device value in the BIOS but won't change anything on the drives.
You should be able to see what device you're booting from currently using a combination of the commands: `glabel status' and 'mount -p'
To change the boot device you need to set it in the BIOS setup using the serial console.
Most importantly though you will only be able to upgrade the firmware there from 23.05.1. 23.09(.1) currently has a bug preventing that. So you if you have that or an earlier version installed to the other boot device you may be to boot to that and run the update. Or if you are running ZFS you can probably roll back to a BE snapshot from 23.05.1 Otherwise you may need to install 23.05.1 in order to run the firmware upgrade.
Open a ticket with us to get the install image for that if you don't have one: https://www.netgate.com/tac-support-request
Steve