Do some tests for us:
Try running your code on USB power. Then on DC plug power. Then try reprogramming your board with only USB power. Then try reprogramming your board with DC plug power connected. What happens?
So as far as you can tell, everything still works but you can't re-program the processor? What power connections do you have (or don't have) plugged in when you try to program it? And what power connections do you have when running it normally?
The chip you circled is the voltage regulator, not a transistor. I ask about the power connections because perhaps you are using different power connections to program it (i.e. USB) and other power connections to run your code normally (maybe the DC barrel jack).
Knowing that the circled chip is a voltage regulator and not a transistor, could you explain one more time what you did when things went up in smoke? Because whenever you say transistor, I am not sure if you are talking about the circled component or the 22222.