I am a bit confused as to your fix.
You ran single board #1 through warmup, then ran single board #2 through warmup, then ran both together?
Sorry if my explanation is too complicated.
1) turn off the miner
2) unplug working board
3) start miner until it hashes.
4) if you are lucky, it will recover bad board
5) turn off miner
6) plug good board back
7) start miner until it hashes.

if you are lucky, you have both working boards
9) if you have bad luck, try it again. You can also try start "single-board-test" program via Putty several times.
NEVER stop or apply changes before miner start hashing. It killed my board, but I recovered it by previous steps.