Does restarting Yún configuration mess up Arduino or its SD card?
It sounds like your SD card has likely failed. Try connecting it to a computer with an SD card reader. If it works at all, back it up immediately if you have files you wish to keep. Then try reading and writing files on it. Also if you have a spare SD card, try to use that in the Yun after setting it up appropriately. That should help narrow down the cause to either the Yun or the SD card.