Hi @jeremy_webb,
Sorry for the delay getting back to you. The link here talks a little about updating the BIOS in standalone mode.
" Updating a Mainboard outside of a laptop
This release supports standalone updates without a battery attached. After rebooting, please follow the onscreen instructions to update your BIOS when in standalone mode, which will require moving the power source between both sides of the Mainboard to allow PD firmware to update correctly if a PD firmware update is necessary."
Some of the firmware for other CPU configurations claim that it will prompt you to do what you need to update the other side of the mainboard. In my experience with the Framework 11th gen boards it never prompted me; so I took the liberty of shutting it down after it said it was complete, pull the power and power the other side of the board and put the USB in to flash the firmware again from the other side of the board.
It sounds crude, however the BIOS updates check to see what version is installed and traditionally will not apply if it already sees the BIOS is the current version.