Not sure about the last bit, but if you send it into nintendo they will probably just replace your MoBo with a patched unit = no more cfw (w/o mod chip, of course)
If you can get into RCM, can you get into Hekate? There is probably a way to get it working again w/o sending it in. I can't really help with that part but there are plenty of people here with the knowledge. You might just have a misconfigured cfw.
If it is some hardware issue, one of the skilled hardware folk could probably repair it for you at a reasonable fee.