6v6gt:
What value resistor was in series with the LED? about 40 Ohms ?
Are you using a Chinese Nano clone ?
If so, the schematic could be like this http://actrl.cz/blog/wp-content/uploads/nano_ch340_schematics.pdf where there is a schottky diode between the USB and Vin. This could have failed under the stress, but I guess the Nano would still work if powered via Vin.
Anyway, the regulator is easy to change (I've done this) and so should the diode be easily changeable.
That Schottky diode actually appears to be between USB +5V and the regulator's output, not Vin. Current can only flow from +5V to Vin as I described earlier. Vin only connects to the regulator's input. (I think you misread the line from the Schottky anode as joining Vin, but it doesn't. There's no blob where they cross. And that would cause a whole raft of other problems if they were joined at that point.)
Edit:
a schottky diode between the USB and Vin
Looking again, I guess you meant "between the USB and +5V". A simple typo makes more sense.
Still, I doubt that the Schottky diode has been damaged. Just the regulator. They don't like conducting backwards. That internal diode can handle a very short surge to 15A, but not very much continuous current at all. Certainly not enough to power a high-current LED.