I solved this for myself and created an account so I could post it here. I saw a few posts going back years which said either this can't be done on an Orange Pi 5 or they had no replies.
The problem:
I wanted to boot my system from the EMMC but leave my large capacity SD card plugged in for extra storage. The script in armbian-config worked as expected. However, leaving the SD card inserted caused the board to continue to boot from it. Wiping the SD prevented the board from booting at all. I could eject the SD card, boot from the EMMC and then re-insert the SD card to use it as storage, but that's annoying.
The solution:
I noticed that the script in armbian-config left the boot partition on the SD card intact but removed the contents. I used the following command to clone the updated EMMC boot partition back to the old boot partition on the SD card-
sudo cat /dev/mmcblk0p1 > /dev/mmcblk1p1
I then wiped the old root partition on the SD card like so-
sudo mkfs.btrfs -f /dev/mmcblk1p2
sudo btrfs filesystem label /dev/mmcblk1p2 SDcard
I rebooted and it worked! I'll add /dev/mmcblk1p2 to fstab so it mounts at boot like a fixed drive.
And I suppose future kernel updates will need to get pushed back to the SD card the same way (similar to updating your bootloader on a x86_64 system after a kernel upgrade). Hopefully I remember this when the board won't boot after the next kernel update. Slackware warns me to update my bootloader when slackpkg updates the kernel, but I know Ubuntu won't. :-)
