I'm have exactly the same problem and I have solve it.
The problem is in bootloader on eMMC. It's locked by default and armbian-config does not unlock it while install on emmc. And the old BOOT0 bootloader can't load new kernel. But we have new bootloader in armbian image. It located in /usr/lib/linux-u-boot-current-bananapim3_20.08.1_armhf/u-boot-sunxi-with-spl.bin in my case. Check your image and fix pathces in further instruction before wiping anything!
So:
1. Flash armbian image to SD, boot normaly and log in (through SSH or phisycal keyboard and monitor - does not matter).
2. We have two boot section on eMMC (mmcblk1boot0 and mmcblk1boot1). I don't know "who is who", so I flash both of them.
Unlock it: echo 0 | sudo tee /sys/block/mmcblk1boot0/force_ro && echo 0 | sudo tee /sys/block/mmcblk1boot1/force_ro
Two zeros in output says it unlocked.
3. Wipe it: sudo dd if=/dev/zero of=/dev/mmcblk1boot0 bs=1k count=1023 seek=1 status=noxfer && sudo dd if=/dev/zero of=/dev/mmcblk1boot1 bs=1k count=1023 seek=1 status=noxfer
4. Now flash new u-boot bootloader into boot partitions:
sudo dd if=/usr/lib/linux-u-boot-current-bananapim3_20.08.1_armhf/u-boot-sunxi-with-spl.bin of=/dev/mmcblk1boot0 bs=1024 seek=8 status=noxfer && sudo dd if=/usr/lib/linux-u-boot-current-bananapim3_20.08.1_armhf/u-boot-sunxi-with-spl.bin of=/dev/mmcblk1boot1 bs=1024 seek=8 status=noxfer
5. Run "sudo armbian-config" and go to: System>Install>Install/Update the bootloader on SD/eMMC (just in case)
Now you can install armbian through armbian-config as usual. After reboot bootloader partition lock by itself. You can check it's blocked by typing: cat /sys/block/mmcblk1boot0/force_ro && cat /sys/block/mmcblk1boot1/force_ro
Output must be like "1 1" in two lines.
