Well, what I did was stupidly try to desolder the programming port to replace it with something else. This ripped out two through-hole on RX and DST, which cut it off from the ATMEGA328P. I *did* have a solution (that worked fine) where I soldered two tiny wires onto the atmega tgfp package and threw a cap between the ftdi driver dtr and reset.
Of course, I am a stupid engineer and cant leave well enough alone, so I tried to get the raspberry pi programming it too. It seems that the trace from the 10 pin header for rx must go over to the programming header before heading to the atmega part because it doesnt connect anymore.
In the process of "fixing" it for that mod, I had resoldered directly to the package too many times, and the trace just doesnt want to pick up more solder.
TL;DR stupid engineer optimizes one too many times :(
Could you post a photo to show the broken point? I may come up with a solution. You could also order a new NyBoard at igg.me/at/nybble.