Thank you very much for your post. You did not only help Hackmodford but also myself. I have opened a new topic that would have fitted into here, but I have linked to your solution.
Arduino Due (or other SAM3/4) upload fails with ATMEL ICE JTAG on VSCode with PlatformIO?
I have previously worked with a combination of notepad++ for editing, Arduino IDE for compiling, and Atmel Studio 7 for uploading .elf/.hex files. But I have obviously missed an integrated IDE that allows debugging with breakpoints. I have tried many times (and failed) to open Arduino Due projects directly in Atmel Studio, as not all of the paths were set correctly. So being able to use an integrated IDE is great!
However, I feel on really thin ice here, as I am not sure what exactly you did with these switch settings that fixed the problem, and I would be completely helpless if I found myself in a similar situation in the future. I hope that not all the debug/upload setups are that cumbersome for every single processor…