Todays results: Failure
I tried to build a recovery after extracing the Nexus 10 CWM recovery and comparing and matching its contents with the stock recovery. I can also flash it using dd, but then the Homesync does not boot anymore, light turns on and off after 1 sec.
Luckly download mode still works and I can re-flash the stock recovery.img to bring it back to life.
I also tried the same for boot.img, I just added a very small file, but when I flash it, same thing happens.
It seems the bootloader has some kind of safety check which checks if the boot.img partition or recovery partition is modified and if so, stops booting
Still could not try updating /system partition manually.