How to mark "not fully installed" apt-get package as "successfully installed"

You should fix /etc/initramfs/post-update.d/flash-kernel so that it successfully flashes your kernel & initrd. It's in /etc, so you're free to edit it to make it work on your board.

If you can't edit it to make it work (e.g., flashing is done with JTAG), then you ought to have it print out a big warning reminding you to flash it, and exit 0.

Once you've fixed it, then you can run dpkg --configure -a.