Fried two Arduino Nano's but works when powered
Judging by your list of observations:


Cannot power through USB
Can power from external source
Can program through USB


it is most likely that the power feed from the USB to the +5V rail has been interrupted.  There is only one component in that link - the diode D1 (an MBR0520).  That is rated at an absolute maximum constant forward current of 0.5A and most USB ports these days are capable of providing far more than that.  A short circuit on the +5V to ground would draw considerably more current than that diode can handle and the Magic Smoke™ would escape.

The diode is on the underside of the Micro and close examination may show a small crack in the surface of it.  That is if it's still there.  I have used a similar PIC32 based board with 0.5A rated diodes on it, and a short of the power rail when powered from USB caused the diode to completely vaporise (at least I could find no trace of it afterwards).