On the barrel connector I accidentally reversed the input voltage to an Arduino Mega. The center post received ground while the outer connection received +12DVC, basically I have the Arduino -12VDC. I have since fixed this problem. When I power the Arduino with the USB I am able to program the Arduino without a problem. When I power the Arduino with the +12VDC the program still runs (confirmed by programming the blink sketch). If I have the +12VDC connected and try to program the Arduino then I get the timeout communication error.

Do I just need to re-burn the bootloader? The Arduino's symptoms match those listed here when both cables are connected: Arduino Mega timeout communication with programmer error

Is there anything else I should verify? Or is the Arduino always going to be damaged?

Also as a note I did the same thing to an Arduino Uno (same rail going to both) and the Uno has no problems when both USB and power are connected.