Thanks to this post I have come a step further:
https://github.com/Sloeber/arduino-eclipse-plugin/issues/892I have now taken version 1.7.0 of bossac, the upload worked right away, even after several attempts.
But unfortunately it still has a very big shortcoming. As soon as I disconnect the DUE from the power supply and reconnect it, the program no longer starts and the LED no longer flashes.
Only when I upload again will it work again.

And one more thing, uploading is only possible at the programming port.
But at least you can now test at least a few programs on the DUO.

I use the following command to upload:
xxx/BOSSA-1.7.0/bin/bossac -e -w -v -b Project1.bin -R
Thanks to this post I have come a step further:
I have now taken version 1.7.0 of bossac, the upload worked right away, even after several attempts.
But unfortunately it still has a very big shortcoming. As soon as I disconnect the DUE from the power supply and reconnect it, the program no longer starts and the LED no longer flashes.
Only when I upload again will it work again.
And one more thing, uploading is only possible at the programming port.
But at least you can now test at least a few programs on the DUO.
I use the following command to upload:
Another thing to note is that the Com port must be reset via DTS, as is the case in the last code.
Whatever else, if you reset the port after uploading, the program will also be stopped, as with the current removal.