You probably trashed the voltage regulator on the first nano, because you were drawing power from it's input, but the power was coming into the system on the regulator's output (the USB power does not go through the voltage regulator, as it's already a regulated 5v, and a linear voltage regulator needs an input voltage higher than the output voltage by some amount (a few tenths of a volt on really nice LDOs, up to 2v for some older models) - So to run at 5v, when supplied by USB, the USB power is connected after the regulator. Thus any voltage on Vin is coming backwards through the regulator via it's internal diode. These diodes are not normally meant to carry continuous current (as this won't happen in normal operation); you probably burned it out.
If you want to power two nano's off of one USB connection, connect the 5v pins, not the Vin pins.
The nano not plugged into USB is probably fine. The one that was plugged into USB is probably usable, but without the onboard voltage regulator (so you can't supply it via Vin)