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.