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Arduino IDE cannot reset the board when firmware is uploaded and reset has to be applied after uploading attempt. The reason for that is that TPS3705 is holding RESET line high (inactive). That makes a whole uploading procedure longer (and frustrating). Add one diode to "isolate" TPS3705 reset pin from Ardino Due RESET line.
Wait, I take that back...once you lift pin 7, and just looking at the pics (and not schematics, which I don't have in front of me), it appears you might have a couple of vias you could solder the diode to. So maybe the pass-thru hole isn't necessary.
I belabor the point only because drilling is irreversible, and if a noob (like me when I'm under caffeinated) makes that kind of mistake, suddenly they're into a much bigger problem...